1JW8

1.3 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF P6 FORM OF MYOGLOBIN

PDB DOI: 10.2210/pdb1JW8/pdb

Classification: OXYGEN STORAGE/TRANSPORT
Organism(s): Physeter catodon
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2001-09-03 Released: 2001-10-10
Deposition Author(s): Phillips Jr., G.N.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.157
R-Value Work: 0.133
R-Value Observed: 0.133

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Sampling of the native conformational ensemble of myoglobin via structures in different crystalline environments.

Kondrashov, D.A., Zhang, W., Aranda, R., Stec, B., Phillips Jr., G.N.

(2008) Proteins 70: 353-362

PubMed: 17680690 Search on PubMed
DOI: 10.1002/prot.21499
Primary Citation of Related Structures:
1JW8, 1U7R, 1U7S

PubMed Abstract:

Proteins sample multiple conformational substates in their native environment, but the process of crystallization selects the conformers that allow for close packing. The population of conformers can be shifted by varying the environment through a range of crystallization conditions, often resulting in different space groups and changes in the packing arrangements. Three high resolution structures of myoglobin (Mb) in different crystal space groups are presented, including one in a new space group P6(1)22 and two structures in space groups P2(1)2(1)2(1) and P6. We compare coordinates and anisotropic displacement parameters (ADPs) from these three structures plus an existing structure in space group P2(1). While the overall changes are small, there is substantial variation in several external regions with varying patterns of crystal contacts across the space group packing arrangements. The structural ensemble containing four different crystal forms displays greater conformational variance (Calpha rmsd of 0.54-0.79 A) in comparison to a collection of four Mb structures with different ligands and mutations in the same crystal form (Calpha rmsd values of 0.28-0.37 A). The high resolution of the data enables comparison of both the magnitudes and directions of ADPs, which are found to be suppressed by crystal contacts. A composite dynamic profile of Mb structural variation from the four structures was compared with an independent structural ensemble developed from NMR refinement. Despite the limitations and biases of each method, the ADPs of the crystallographic ensemble closely match the positional variance from the solution NMR ensemble with linear correlation of 0.8. This suggests that crystal packing selects conformers representative of the solution ensemble, and several different crystal forms give a more complete view of the plasticity of a protein structure.

Organizational Affiliation:

Department of Biochemistry, University of Wisconsin - Madison, Madison, Wisconsin 53706, USA.

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
MYOGLOBIN	A	154	Physeter catodon	Mutation(s): 0 Gene Names: MB (Synthesized), MB
UniProt
Find proteins for P02185 (Physeter macrocephalus) Explore P02185 Go to UniProtKB: P02185
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P02185
Protein Feature View 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 E [auth A] MOL2 format, chain E [auth A]	E [auth A]	PROTOPORPHYRIN IX CONTAINING FE C₃₄ H₃₂ Fe N₄ O₄ KABFMIBPWCXCRK-RGGAHWMASA-L		Ligand Interaction
SO4 Query on SO4 Download Ideal Coordinates CCD File SDF format, chain B [auth A] SDF format, chain C [auth A] SDF format, chain D [auth A] MOL2 format, chain B [auth A] MOL2 format, chain C [auth A] MOL2 format, chain D [auth A]	B [auth A], C [auth A], D [auth A]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Ligand Interaction
CMO Query on CMO Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	CARBON MONOXIDE C O UGFAIRIUMAVXCW-UHFFFAOYSA-N		Ligand Interaction

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.30 Å
R-Value Free: 0.157
R-Value Work: 0.133
R-Value Observed: 0.133
Space Group: P 6

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 90.38	α = 90
b = 90.38	β = 90
c = 45.34	γ = 120

Software Package:

Software Name	Purpose
MERLOT	phasing
SHELXL-97	refinement
DENZO	data reduction
SCALEPACK	data scaling

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Deposited Date: 2001-09-03
Released Date: 2001-10-10

Deposition Author(s):

Phillips Jr., G.N.

Revision History (Full details and data files)

Version 1.0: 2001-10-10
Type: Initial release
Version 1.1: 2008-04-27
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Derived calculations, Version format compliance
Version 1.3: 2013-01-30
Changes: Database references, Structure summary
Version 1.4: 2017-10-04
Changes: Refinement description