2R50 | pdb_00002r50

The crystal structure of nonsymbiotic corn hemoglobin 1

PDB DOI: https://doi.org/10.2210/pdb2R50/pdb

Classification: METAL BINDING PROTEIN
Organism(s): Zea mays subsp. parviglumis
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2007-09-02 Released: 2007-09-18
Deposition Author(s): Smagghe, B.J., Hoy, J.A., Hargrove, M.S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free:
0.253 (Depositor), 0.250 (DCC)
R-Value Work:
0.201 (Depositor), 0.200 (DCC)
R-Value Observed:
0.203 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

This is version 1.2 of the entry. See complete history.

Literature

The crystal structure of nonsymbiotic corn hemoglobin 1

Smagghe, B.J., Hoy, J.A., Hargrove, M.S.

To be published.

Macromolecule Content

Total Structure Weight: 76.28 kDa
Atom Count: 5,368
Modeled Residue Count: 584
Deposited Residue Count: 660
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Non-symbiotic hemoglobin	A, B, C, D	165	Zea mays subsp. parviglumis	Mutation(s): 0 Gene Names: HB, GLB1 EC: 1.7.2
UniProt
Find proteins for Q9M593 (Zea mays subsp. parviglumis) Explore Q9M593 Go to UniProtKB: Q9M593
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q9M593
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download Ideal Coordinates CCD File SDF format, chain N [auth D] SDF format, chain K [auth C] SDF format, chain G [auth B] SDF format, chain E [auth A] MOL2 format, chain N [auth D] MOL2 format, chain K [auth C] MOL2 format, chain G [auth B] MOL2 format, chain E [auth A] mmCIF format, chain N [auth D] mmCIF format, chain K [auth C] mmCIF format, chain G [auth B] mmCIF format, chain E [auth A]	E [auth A], G [auth B], K [auth C], N [auth D]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C] Focus chain N [auth D] Interactions & Density Focus chain E [auth A] Focus chain G [auth B] Focus chain K [auth C] Focus chain N [auth D]
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain M [auth D] SDF format, chain L [auth D] SDF format, chain J [auth C] SDF format, chain I [auth C] SDF format, chain F [auth B] MOL2 format, chain M [auth D] MOL2 format, chain L [auth D] MOL2 format, chain J [auth C] MOL2 format, chain I [auth C] MOL2 format, chain F [auth B] mmCIF format, chain M [auth D] mmCIF format, chain L [auth D] mmCIF format, chain J [auth C] mmCIF format, chain I [auth C] mmCIF format, chain F [auth B]	F [auth B], I [auth C], J [auth C], L [auth D], M [auth D]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain F [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth D] Interactions & Density Focus chain F [auth B] Focus chain I [auth C] Focus chain J [auth C] Focus chain L [auth D] Focus chain M [auth D]
ACY Query on ACY Download Ideal Coordinates CCD File SDF format, chain O [auth D] SDF format, chain H [auth B] MOL2 format, chain O [auth D] MOL2 format, chain H [auth B] mmCIF format, chain O [auth D] mmCIF format, chain H [auth B]	H [auth B], O [auth D]	ACETIC ACID C₂ H₄ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-N		Interactions Focus chain H [auth B] Focus chain O [auth D] Interactions & Density Focus chain H [auth B] Focus chain O [auth D]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.20 Å
R-Value Free: 0.253 (Depositor), 0.250 (DCC)
R-Value Work: 0.201 (Depositor), 0.200 (DCC)
R-Value Observed: 0.203 (Depositor)

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 50.754	α = 90
b = 89.734	β = 90
c = 157.424	γ = 90

Software Package:

Software Name	Purpose
d*TREK	data scaling
AMoRE	phasing
REFMAC	refinement
PDB_EXTRACT	data extraction
CrystalClear	data collection
d*TREK	data reduction

Structure Validation

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Entry History

Deposition Data

Released Date: 2007-09-18

Deposition Author(s):

Smagghe, B.J.

Hoy, J.A.

Hargrove, M.S.

Revision History (Full details and data files)

Version 1.0: 2007-09-18
Type: Initial release
Version 1.1: 2011-07-13
Changes: Version format compliance
Version 1.2: 2023-08-30
Changes: Data collection, Database references, Derived calculations, Refinement description

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Help and Resources

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The crystal structure of nonsymbiotic corn hemoglobin 1

The crystal structure of nonsymbiotic corn hemoglobin 1

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

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Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)

2R50 | pdb_00002r50