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- PDB-1k47: Crystal Structure of the Streptococcus pneumoniae Phosphomevalona... -

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Basic information

Entry
Database: PDB / ID: 1k47
TitleCrystal Structure of the Streptococcus pneumoniae Phosphomevalonate Kinase (PMK)
Componentsphosphomevalonate kinase
KeywordsTRANSFERASE / Alpha/beta single domain belonging to the GHMP kinase superfamily / MvaK2 / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


phosphomevalonate kinase / isopentenyl diphosphate biosynthetic process, mevalonate pathway / kinase activity / phosphorylation / ATP binding / membrane
Similarity search - Function
Phosphomevalonate kinase, bacteria / Phosphomevalonate kinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 ...Phosphomevalonate kinase, bacteria / Phosphomevalonate kinase / GHMP kinase, C-terminal domain / GHMP kinases C terminal / GHMP kinase, C-terminal domain / GHMP kinase N-terminal domain / GHMP kinases N terminal domain / GHMP kinase, C-terminal domain superfamily / Ribosomal Protein S5; domain 2 - #10 / Ribosomal Protein S5; domain 2 / Ribosomal protein S5 domain 2-type fold, subgroup / Ribosomal protein S5 domain 2-type fold / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
phosphomevalonate kinase
Similarity search - Component
Biological speciesStreptococcus pneumoniae R6 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Single anomalous scattering / Resolution: 2.42 Å
AuthorsRomanowski, M.J. / Bonanno, J.B. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: Proteins / Year: 2002
Title: Crystal structure of the Streptococcus pneumoniae phosphomevalonate kinase, a member of the GHMP kinase superfamily.
Authors: Romanowski, M.J. / Bonanno, J.B. / Burley, S.K.
History
DepositionOct 5, 2001Deposition site: RCSB / Processing site: RCSB
Revision 1.0May 8, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations ...Database references / Derived calculations / Refinement description / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / software / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _software.classification / _software.name / _software.version / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: phosphomevalonate kinase
B: phosphomevalonate kinase
C: phosphomevalonate kinase
D: phosphomevalonate kinase
E: phosphomevalonate kinase
F: phosphomevalonate kinase


Theoretical massNumber of molelcules
Total (without water)226,2416
Polymers226,2416
Non-polymers00
Water14,034779
1
A: phosphomevalonate kinase


Theoretical massNumber of molelcules
Total (without water)37,7071
Polymers37,7071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: phosphomevalonate kinase


Theoretical massNumber of molelcules
Total (without water)37,7071
Polymers37,7071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: phosphomevalonate kinase


Theoretical massNumber of molelcules
Total (without water)37,7071
Polymers37,7071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
4
D: phosphomevalonate kinase


Theoretical massNumber of molelcules
Total (without water)37,7071
Polymers37,7071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
5
E: phosphomevalonate kinase


Theoretical massNumber of molelcules
Total (without water)37,7071
Polymers37,7071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
6
F: phosphomevalonate kinase


Theoretical massNumber of molelcules
Total (without water)37,7071
Polymers37,7071
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)231.606, 231.606, 88.587
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number173
Space group name H-MP63
DetailsThe protein is a monomer in solution and crystallizes as a hexameric asymetric unit of 3/222 noncrystallographic symmetry

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Components

#1: Protein
phosphomevalonate kinase


Mass: 37706.867 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae R6 (bacteria) / Species: Streptococcus pneumoniae / Strain: ATCC BAA-255 / R6 / Gene: mvaK2 / Plasmid: pGEX6P-1 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q8DR49, phosphomevalonate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 779 / 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: 3.14 Å3/Da / Density % sol: 60.5 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: sodium dihydrogen phosphate, potassium dihydrogen phosphate, HEPES, ATP, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 7
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
124 mg/mlprotein1drop
220 mMHEPES1droppH7.0
3100 mM1dropKCl
43 mMdithiothreitol1drop
50.1 MHEPES1reservoirpH7.5
60.8 Msodium phosphate1reservoir
70.8 Mpotassium phosphate1reservoir
830 mMATP1reservoirunbuffered

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X25 / Wavelength: 0.9792 Å
DetectorType: BRANDEIS - B4 / Detector: CCD / Date: Feb 28, 2001
Details: 27-pole hybrid wiggler and vertical focusing mirror
RadiationMonochromator: double Si crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.4→20 Å / Num. all: 202265 / Num. obs: 198856 / % possible obs: 98.3 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 6.8 % / Biso Wilson estimate: 46 Å2 / Rmerge(I) obs: 0.082 / Rsym value: 0.082 / Net I/σ(I): 24.1
Reflection shellResolution: 2.4→2.49 Å / Rmerge(I) obs: 0.409 / Mean I/σ(I) obs: 2.5 / Num. unique all: 18706 / Rsym value: 0.409 / % possible all: 92.3
Reflection
*PLUS
Highest resolution: 2.4 Å / Lowest resolution: 20 Å / Num. obs: 103387 / Num. measured all: 3616027 / Rmerge(I) obs: 0.082
Reflection shell
*PLUS
% possible obs: 92.4 % / Rmerge(I) obs: 0.409

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Processing

Software
NameVersionClassification
SnBphasing
MLPHAREphasing
DMmodel building
CNS1refinement
DENZOdata reduction
SCALEPACKdata scaling
DMphasing
RefinementMethod to determine structure: Single anomalous scattering / Resolution: 2.42→20 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
Details: anomalous scattering correction applied for 48 Se sites
RfactorNum. reflection% reflectionSelection details
Rfree0.257 18573 -random
Rwork0.215 ---
all0.217 192349 --
obs0.217 192349 95 %-
Displacement parameters
Baniso -1Baniso -2Baniso -3
1-1.528 Å2-5.718 Å20 Å2
2--1.528 Å20 Å2
3----3.055 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.3 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.32 Å
Refinement stepCycle: LAST / Resolution: 2.42→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms15000 0 0 779 15779
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0066
X-RAY DIFFRACTIONc_angle_deg1.319
X-RAY DIFFRACTIONc_mcbond_it1.348
X-RAY DIFFRACTIONc_mcangle_it2.272
X-RAY DIFFRACTIONc_scbond_it3.162
X-RAY DIFFRACTIONc_scangle_it4.025
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkRefine-IDNum. reflection obs
2.42-2.440.3122590.305X-RAY DIFFRACTION2983
8.67-200.2093680.172X-RAY DIFFRACTION4055
Refinement
*PLUS
Lowest resolution: 20 Å / % reflection Rfree: 9.2 % / Rfactor all: 0.217 / Rfactor obs: 0.215 / Rfactor Rfree: 0.257 / Rfactor Rwork: 0.215
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.32
LS refinement shell
*PLUS
Rfactor Rfree: 0.312 / Rfactor Rwork: 0.305 / Rfactor obs: 0.305

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