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- PDB-1v6s: Crystal Structure of Phosphoglycerate Kinase from Thermus thermop... -

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Basic information

Entry
Database: PDB / ID: 1v6s
TitleCrystal Structure of Phosphoglycerate Kinase from Thermus thermophilus HB8
ComponentsPhosphoglycerate kinase
KeywordsTRANSFERASE / phosphoglycerate kinase / Thermus thermophilus / RIKEN Structural Genomics/Proteomics Initiative / RSGI / Structural Genomics
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
Phosphoglycerate kinase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.5 Å
AuthorsMizutani, H. / Kunishima, N. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal Structure of Phosphoglycerate Kinase from Thermus thermophilus HB8
Authors: Mizutani, H. / Kunishima, N.
History
DepositionDec 4, 2003Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 23, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Oct 25, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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
B: Phosphoglycerate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,0999
Polymers83,6622
Non-polymers4377
Water13,223734
1
A: Phosphoglycerate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0384
Polymers41,8311
Non-polymers2073
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Phosphoglycerate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,0615
Polymers41,8311
Non-polymers2304
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)143.175, 143.175, 75.641
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number170
Space group name H-MP65
DetailsThe biological assembly is a monomer.

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Components

#1: Protein Phosphoglycerate kinase


Mass: 41831.023 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 (DE3) / References: UniProt: P09403, phosphoglycerate kinase
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Na
#3: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 734 / 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: 2.7 Å3/Da / Density % sol: 54.05 %
Crystal growTemperature: 291 K / Method: microbatch / pH: 5.3
Details: sodium formate, acetate, pH 5.3, microbatch, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 1 Å
DetectorType: RIGAKU RAXIS V / Detector: IMAGE PLATE / Date: Oct 18, 2003 / Details: mirrors
RadiationMonochromator: MIRRORS / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.5→30 Å / Num. all: 140815 / Num. obs: 140815 / % possible obs: 99.9 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.46 % / Biso Wilson estimate: 17.1 Å2 / Rmerge(I) obs: 0.051 / Rsym value: 0.044 / Net I/σ(I): 21.4
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 5.38 % / Rmerge(I) obs: 0.192 / Mean I/σ(I) obs: 7.89 / Num. unique all: 13920 / Rsym value: 0.169 / % possible all: 99.3

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VPE

1vpe


Resolution: 1.5→30 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 2567263.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.215 7031 5 %RANDOM
Rwork0.201 ---
all0.202 140815 --
obs0.202 140777 99.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 54.829 Å2 / ksol: 0.374112 e/Å3
Displacement parametersBiso mean: 19.1 Å2
Baniso -1Baniso -2Baniso -3
1-0.31 Å20.49 Å20 Å2
2--0.31 Å20 Å2
3----0.62 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.19 Å0.17 Å
Luzzati d res low-5 Å
Luzzati sigma a0.11 Å0.09 Å
Refinement stepCycle: LAST / Resolution: 1.5→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5898 0 27 734 6659
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_d23.6
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_mcbond_it1.031.5
X-RAY DIFFRACTIONc_mcangle_it1.582
X-RAY DIFFRACTIONc_scbond_it1.842
X-RAY DIFFRACTIONc_scangle_it2.712.5
LS refinement shellResolution: 1.5→1.55 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 10
RfactorNum. reflection% reflection
Rfree0.247 721 5.2 %
Rwork0.223 13162 -
obs--99 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ION.PARAMION.TOP
X-RAY DIFFRACTION4GOL.PARAMGOL.TOP

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