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- PDB-3r7a: Crystal structure of phosphoglycerate mutase from Bacillus anthra... -

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Basic information

Entry
Database: PDB / ID: 3r7a
TitleCrystal structure of phosphoglycerate mutase from Bacillus anthracis str. Sterne
ComponentsPhosphoglycerate mutase, putative
KeywordsTRANSFERASE / Structural Genomics / PSI-Biology / Midwest Center for Structural Genomics / MCSG / phosphoglycerate mutase / catalyzes the internal transfer of a phosphate group from C-3 to C-2 which results in the conversion of 3-phosphoglycerate (3PG) to 2-phosphoglycerate (2PG)
Function / homology
Function and homology information


phosphoglycerate mutase activity / glycolytic process
Similarity search - Function
Phosphoglycerate mutase family / Phosphoglycerate mutase-like / Histidine phosphatase superfamily, clade-1 / Histidine phosphatase superfamily (branch 1) / Histidine phosphatase superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Histidine phosphatase family protein / Putative phosphoglycerate mutase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.845 Å
AuthorsChang, C. / Chhor, G. / Clancy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: Crystal structure of phosphoglycerate mutase from Bacillus anthracis str. Sterne
Authors: Chang, C. / Chhor, G. / Clancy, S. / Joachimiak, A.
History
DepositionMar 22, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 20, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Phosphoglycerate mutase, putative
B: Phosphoglycerate mutase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,1694
Polymers52,6922
Non-polymers4772
Water5,801322
1
A: Phosphoglycerate mutase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5842
Polymers26,3461
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Phosphoglycerate mutase, putative
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,5842
Polymers26,3461
Non-polymers2381
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)101.435, 101.435, 88.936
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number96
Space group name H-MP43212
Components on special symmetry positions
IDModelComponents
11A-375-

HOH

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Components

#1: Protein Phosphoglycerate mutase, putative / / Putative phosphoglycerate mutase


Mass: 26346.025 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS3287, BA_3545, GBAA3545, GBAA_3545 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)magic / References: UniProt: Q81YJ8, UniProt: A0A6L8PQE4*PLUS
#2: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES / HEPES


Mass: 238.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 322 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.17 Å3/Da / Density % sol: 43.34 %
Crystal growTemperature: 297 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 0.1M Bis-Tris Propane pH 7.0, 2.5 M Ammonium Sulfate, VAPOR DIFFUSION, SITTING DROP, temperature 297K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97912 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Dec 9, 2010
RadiationMonochromator: Si(111) double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97912 Å / Relative weight: 1
ReflectionResolution: 1.845→71.725 Å / Num. all: 40475 / Num. obs: 40445 / % possible obs: 99.9 % / Observed criterion σ(I): -3 / Redundancy: 16.1 % / Rmerge(I) obs: 0.097 / Net I/σ(I): 46.4
Reflection shellResolution: 1.845→1.88 Å / Redundancy: 15.3 % / Rmerge(I) obs: 0.747 / Mean I/σ(I) obs: 4 / Num. unique all: 1967 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.5.0109refinement
PDB_EXTRACT3.1data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
HKL-3000phasing
MLPHAREphasing
DMphasing
SHELXDEphasing
RESOLVEphasing
ARP/wARPmodel building
Cootmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.845→71.725 Å / Cor.coef. Fo:Fc: 0.963 / Cor.coef. Fo:Fc free: 0.947 / Occupancy max: 1 / Occupancy min: 0.3 / SU B: 5.948 / SU ML: 0.082 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.412 / ESU R Free: 0.124
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2043 2026 5 %RANDOM
Rwork0.1622 ---
all0.1643 40380 --
obs0.1643 40380 99.91 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 90.71 Å2 / Biso mean: 30.9778 Å2 / Biso min: 15.21 Å2
Baniso -1Baniso -2Baniso -3
1--1.4 Å20 Å20 Å2
2---1.4 Å20 Å2
3---2.79 Å2
Refinement stepCycle: LAST / Resolution: 1.845→71.725 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3516 0 30 322 3868
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0223758
X-RAY DIFFRACTIONr_angle_refined_deg1.3621.9745091
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.445486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.69225.879165
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.96115710
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.771516
X-RAY DIFFRACTIONr_chiral_restr0.0950.2580
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.022774
X-RAY DIFFRACTIONr_mcbond_it1.3231.52344
X-RAY DIFFRACTIONr_mcangle_it2.26323793
X-RAY DIFFRACTIONr_scbond_it3.37931414
X-RAY DIFFRACTIONr_scangle_it5.2794.51298
X-RAY DIFFRACTIONr_rigid_bond_restr1.64833758
LS refinement shellResolution: 1.845→1.893 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.256 147 -
Rwork0.171 2708 -
all-2855 -
obs-2855 99.76 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
10.47240.2843-0.14260.3648-0.05320.0486-0.00690.0022-0.01470.00340.0005-0.00060.0026-0.00050.00650.0160.0040.00090.01360.00120.00756.85518.903827.342
20.40160.02420.20010.222-0.01960.2928-0.0107-0.03750.03620.00640.00010.0159-0.0254-0.00940.01070.0180.00230.00080.0149-0.00390.015912.753843.26221.0015
30.03810.00870.01470.0161-0.01530.0311-0.0003-0.00420.0053-0.0007-0.0009-0.00020.0002-0.00060.00120.01760.00030.0010.01910.00050.0121-2.403726.082123.6011
40.08780.00870.00950.21720.0880.1085-0.0051-0.00020.0155-0.0010.00540.0031-0.01310.0028-0.00030.0140.0008-0.00140.017400.0162-23.317136.18156.7498
50.15490.129-0.21650.2484-0.170.329-0.0046-0.0176-0.0172-0.0119-0.0087-0.01720.01360.0240.01320.015-0.00010.00270.020.00010.0089-13.291119.0124-9.8066
60.1713-0.0217-0.0460.06040.02290.1761-0.0010.00860.0425-0.0044-0.0036-0.0087-0.01270.01710.00460.0139-0.00410.00040.01430.00140.0245-12.113438.84972.5714
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 94
2X-RAY DIFFRACTION2A95 - 147
3X-RAY DIFFRACTION3A148 - 230
4X-RAY DIFFRACTION4B5 - 94
5X-RAY DIFFRACTION5B95 - 147
6X-RAY DIFFRACTION6B148 - 232

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