6SVA | pdb_00006sva

Multicrystal structure of equine Haemoglobin at room temperature using a multilayer monochromator.

PDB DOI: https://doi.org/10.2210/pdb6SVA/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Equus caballus
Mutation(s): No

Deposited: 2019-09-18 Released: 2019-11-20
Deposition Author(s): Sandy, J., Sanchez-Weatherby, J., Mikolajek, H., Lewis, G., Angus, R.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free:
0.173 (Depositor), 0.175 (DCC)
R-Value Work:
0.141 (Depositor), 0.143 (DCC)
R-Value Observed:
0.142 (Depositor)

Starting Model: experimental
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Ligand Structure Quality Assessment

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

Literature

Protein-to-structure pipeline for ambient-temperature crystallography at VMXi

Mikolajek, H., Sanchez-Weatherby, J., Sandy, J., Gildea, R.G., Campeotto, I., Cheruvara, H., Clarke, J.D., Foster, T., Fujii, S., Paulsen, I.T., Shah, B.S., Hough, M.A.

(2023) IUCrJ

DOI: https://doi.org/10.1107/S2052252523003810

Macromolecule Content

Total Structure Weight: 32.25 kDa
Atom Count: 2,420
Modeled Residue Count: 285
Deposited Residue Count: 286
Unique protein chains: 2

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit alpha	A	140	Equus caballus	Mutation(s): 0
UniProt
Find proteins for P01958 (Equus caballus) Explore P01958 Go to UniProtKB: P01958
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P01958
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Hemoglobin subunit beta	B	146	Equus caballus	Mutation(s): 0
UniProt
Find proteins for P02062 (Equus caballus) Explore P02062 Go to UniProtKB: P02062
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P02062
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
HEM Query on HEM Download:Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.92 Å
R-Value Free: 0.173 (Depositor), 0.175 (DCC)
R-Value Work: 0.141 (Depositor), 0.143 (DCC)
R-Value Observed: 0.142 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 108.515	α = 90
b = 62.992	β = 111.051
c = 54.591	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
PHENIX	refinement
DIALS	data reduction
xia2	data scaling
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

Deposition Data

Released Date: 2019-11-20

Deposition Author(s):

Sanchez-Weatherby, J.

Revision History (Full details and data files)

Version 1.0: 2019-11-20
Type: Initial release
Version 1.1: 2023-05-17
Changes: Database references, Derived calculations
Version 1.2: 2024-02-07
Changes: Data collection, Refinement description

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.