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- PDB-3uwd: Crystal Structure of Phosphoglycerate Kinase from Bacillus Anthracis -

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Basic information

Entry
Database: PDB / ID: 3uwd
TitleCrystal Structure of Phosphoglycerate Kinase from Bacillus Anthracis
ComponentsPhosphoglycerate kinase
KeywordsTRANSFERASE / Anthrax / Structural Genomics / Center for Structural Genomics of Infectious Diseases / CSGID / Rossmann fold / phosphoglycerate kinase / phosphoglycerate / Phosphorylation
Function / homology
Function and homology information


phosphoglycerate kinase / phosphoglycerate kinase activity / glycolytic process / ATP binding / cytoplasm
Similarity search - Function
Phosphoglycerate kinase, N-terminal domain / Phosphoglycerate kinase / Phosphoglycerate kinase, N-terminal / Phosphoglycerate kinase, conserved site / Phosphoglycerate kinase superfamily / Phosphoglycerate kinase / Phosphoglycerate kinase signature. / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Unknown ligand / Phosphoglycerate kinase
Similarity search - Component
Biological speciesBacillus anthracis (anthrax bacterium)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.68 Å
AuthorsZheng, H. / Chruszcz, M. / Porebski, P. / Kudritska, M. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Minor, W. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: J.Struct.Funct.Genom. / Year: 2012
Title: Crystal structures of putative phosphoglycerate kinases from B. anthracis and C. jejuni.
Authors: Zheng, H. / Filippova, E.V. / Tkaczuk, K.L. / Dworzynski, P. / Chruszcz, M. / Porebski, P.J. / Wawrzak, Z. / Onopriyenko, O. / Kudritska, M. / Grimshaw, S. / Savchenko, A. / Anderson, W.F. / Minor, W.
History
DepositionDec 1, 2011Deposition site: RCSB / Processing site: RCSB
SupersessionJan 11, 2012ID: 3B2B
Revision 1.0Jan 11, 2012Provider: repository / Type: Initial release
Revision 1.1May 23, 2012Group: Database references
Revision 1.2Apr 13, 2022Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr2_auth_seq_id / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phosphoglycerate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)43,2939
Polymers42,8821
Non-polymers4118
Water6,035335
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Phosphoglycerate kinase
hetero molecules

A: Phosphoglycerate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,58618
Polymers85,7652
Non-polymers82216
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area4670 Å2
ΔGint-107 kcal/mol
Surface area30550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)119.687, 45.334, 68.607
Angle α, β, γ (deg.)90.00, 97.95, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-395-

CL

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Phosphoglycerate kinase


Mass: 42882.320 Da / Num. of mol.: 1 / Mutation: T190A
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bacillus anthracis (anthrax bacterium) / Strain: Sterne / Gene: BAS4988, BA_5367, GBAA_5367, pgk / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-CodonPlus(DE3)-RIPL / References: UniProt: Q81X75, phosphoglycerate kinase

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Non-polymers , 5 types, 343 molecules

#2: Chemical
ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-BTB / 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / BIS-TRIS BUFFER


Mass: 209.240 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H19NO5 / Comment: pH buffer*YM
#5: Chemical ChemComp-UNL / UNKNOWN LIGAND


Num. of mol.: 1 / Source method: obtained synthetically
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 335 / 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: 2.15 Å3/Da / Density % sol: 42.73 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 25% PEG 3350, 0.2M NaCl, 0.1M Bis-Tris, 2% Hexandiol, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-F / Wavelength: 0.979 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 8, 2010 / Details: BERYLLIUM LENSES
RadiationMonochromator: DIAMOND [111] / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.68→50 Å / Num. all: 41651 / Num. obs: 41594 / % possible obs: 99.9 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.1 % / Biso Wilson estimate: 16.368 Å2 / Rmerge(I) obs: 0.039 / Rsym value: 0.039 / Net I/σ(I): 24.38
Reflection shellResolution: 1.68→1.69 Å / Redundancy: 4 % / Rmerge(I) obs: 0.398 / Mean I/σ(I) obs: 2.2 / Num. unique all: 996 / Rsym value: 0.398 / % possible all: 99.4

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Processing

Software
NameVersionClassification
MD2diffractometer softwaredata collection
HKL-3000SHELXC/D/Ephasing
MLPHAREphasing
DMmodel building
ARP/wARPmodel building
RESOLVEmodel building
CCP4model building
REFMAC5.6.0117refinement
HKL-2000data reduction
HKL-2000data scaling
DMphasing
RESOLVEphasing
CCP4phasing
RefinementMethod to determine structure: SAD / Resolution: 1.68→50 Å / Cor.coef. Fo:Fc: 0.958 / Cor.coef. Fo:Fc free: 0.941 / SU B: 4.191 / SU ML: 0.074 / Isotropic thermal model: Isotropic / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.12 / ESU R Free: 0.116 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2132 1924 5.1 %RANDOM
Rwork0.1739 ---
all0.1759 41651 --
obs0.1759 35939 90.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 25.911 Å2
Baniso -1Baniso -2Baniso -3
1--0.75 Å20 Å2-0.44 Å2
2--0.64 Å20 Å2
3----0.01 Å2
Refinement stepCycle: LAST / Resolution: 1.68→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2939 0 28 335 3302
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0193136
X-RAY DIFFRACTIONr_bond_other_d0.0010.022125
X-RAY DIFFRACTIONr_angle_refined_deg1.5912.0054262
X-RAY DIFFRACTIONr_angle_other_deg2.27335246
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3645427
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.51825.391128
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.94815521
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.2151514
X-RAY DIFFRACTIONr_chiral_restr0.0940.2486
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.0213545
X-RAY DIFFRACTIONr_gen_planes_other0.0050.02589
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.682→1.725 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.215 80 -
Rwork0.213 1412 -
obs-1488 49.93 %
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)
16.4287-0.9621.914.0939-0.91083.3287-0.2485-0.89940.26480.43570.1475-0.1797-0.09920.01870.1010.10940.1098-0.05990.2457-0.04720.194327.89525.82220.537
26.7048-2.37181.23891.0173-0.73341.3402-0.02990.25990.4427-0.0562-0.0856-0.120.12970.27740.11550.090.0586-0.03130.1460.02440.229430.16726.12610.718
31.9361-0.07080.21051.7091-0.06981.45570.0526-0.0533-0.3095-0.04290.1119-0.02380.0849-0.0269-0.16450.0741-0.00350.00810.03330.02820.09951.94934.39310.81
40.97610.73430.54813.33420.78461.6331-0.0113-0.0537-0.0667-0.19120.09270.0671-0.267-0.2307-0.08130.12680.04030.04470.08290.02670.0356-4.61849.9219.315
50.58840.04440.23692.13930.95221.32050.0501-0.2133-0.12820.1403-0.0025-0.0238-0.0109-0.1566-0.04770.10880.01780.0350.14330.06220.0548-2.01843.82924.278
66.8185-6.03790.72855.83770.15281.88570.17930.1645-0.107-0.0525-0.0356-0.10760.11740.1012-0.14380.12230.0154-0.05670.1025-0.01880.230313.09329.2246.434
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 95
2X-RAY DIFFRACTION2A96 - 172
3X-RAY DIFFRACTION3A173 - 210
4X-RAY DIFFRACTION4A211 - 255
5X-RAY DIFFRACTION5A256 - 372
6X-RAY DIFFRACTION6A373 - 394

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