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- PDB-1to6: Glycerate kinase from Neisseria meningitidis (serogroup A) -

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Basic information

Entry
Database: PDB / ID: 1to6
TitleGlycerate kinase from Neisseria meningitidis (serogroup A)
ComponentsGlycerate kinase
KeywordsTRANSFERASE / GLYCERATE METABOLISM / STRUCTURAL GENOMICS T831 / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


glycerate 3-kinase / organic acid phosphorylation / glycerate kinase activity / ATP binding
Similarity search - Function
Glycerate kinase; domain 1 / Glycerate kinase, domain 2 / Glycerate kinase, domain 2 / Glycerate kinase / Glycerate kinase, flavodoxin-like fold / Glycerate kinase, restriction-enzyme-like fold / Glycerate kinase superfamily / Glycerate kinase family / Alpha-Beta Complex / Rossmann fold ...Glycerate kinase; domain 1 / Glycerate kinase, domain 2 / Glycerate kinase, domain 2 / Glycerate kinase / Glycerate kinase, flavodoxin-like fold / Glycerate kinase, restriction-enzyme-like fold / Glycerate kinase superfamily / Glycerate kinase family / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Biological speciesNeisseria meningitidis serogroup A (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.5 Å
AuthorsRajashankar, K.R. / Kniewel, R. / Solorzano, V. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Glycerate kinase from Neisseria meningitidis (serogroup A)
Authors: RAJASHANKAR, K.R. / KNIEWEL, R. / SOLORZANO, V. / LIMA, C.D.
History
DepositionJun 13, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 3, 2021Group: Derived calculations / Structure summary / Category: audit_author / struct_site
Item: _audit_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id ..._audit_author.identifier_ORCID / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Remark 999SEQUENCE RESIDUE B329 IS DISALLOWED, BUT ELECTRON DENSITY CLEARLY INDICATES THIS CONFORMATION.
Remark 600HETEROGEN SULFATES 302,303,304,305 MARK ACTIVE SITE, POTENTIAL ATP BINDING SITE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Glycerate kinase
B: Glycerate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,7078
Polymers79,1302
Non-polymers5766
Water3,513195
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4320 Å2
ΔGint-120 kcal/mol
Surface area30480 Å2
MethodPISA
2
A: Glycerate kinase
B: Glycerate kinase
hetero molecules

A: Glycerate kinase
B: Glycerate kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)159,41316
Polymers158,2604
Non-polymers1,15312
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,y,-z1
Buried area13060 Å2
ΔGint-273 kcal/mol
Surface area56550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.767, 77.386, 101.436
Angle α, β, γ (deg.)90.00, 107.41, 90.00
Int Tables number5
Space group name H-MC121
DetailsUNCONFIRMED DIMER AS REPRESENTED IN THE ASU

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Components

#1: Protein Glycerate kinase


Mass: 39565.109 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Neisseria meningitidis serogroup A (bacteria)
Species: Neisseria meningitidis / Strain: serogroup A / Gene: GLXK, NMA1473 / Plasmid: PET T7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21 DE3 / References: UniProt: P57098, glycerate 3-kinase
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 2.5 Å3/Da / Density % sol: 50.84 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 4.5
Details: 21% PEG MME 2K, 0.1M SODIUM CITRATE, 0.2M AMMONIUM SULFATE, pH 4.5, VAPOR DIFFUSION, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.979 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 27, 2003 / Details: MIRRORS
RadiationMonochromator: DIAMOND / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→20 Å / Num. all: 34873 / Num. obs: 34350 / % possible obs: 97 % / Observed criterion σ(F): -2 / Observed criterion σ(I): -2 / Biso Wilson estimate: 57.5 Å2
Reflection shellResolution: 2.3→2.38 Å / % possible all: 89.1

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.5→19.76 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2273581.73 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.283 1345 5 %RANDOM
Rwork0.226 ---
obs0.226 26940 99.3 %-
all-27130 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 41.1273 Å2 / ksol: 0.327692 e/Å3
Displacement parametersBiso mean: 54 Å2
Baniso -1Baniso -2Baniso -3
1-18.66 Å20 Å2-1.44 Å2
2--3.83 Å20 Å2
3----22.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati d res low-6 Å
Luzzati sigma a0.45 Å0.33 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5552 0 30 195 5777
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_dihedral_angle_d23.9
X-RAY DIFFRACTIONc_improper_angle_d0.79
X-RAY DIFFRACTIONc_mcbond_it1.581.5
X-RAY DIFFRACTIONc_mcangle_it2.712
X-RAY DIFFRACTIONc_scbond_it2.122
X-RAY DIFFRACTIONc_scangle_it3.222.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.029 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.413 208 4.7 %
Rwork0.314 4191 -
obs--98.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2DNA-RNA_REP.PARAMDNA-RNA.TOP
X-RAY DIFFRACTION3WATER_REP.PARAMWATER.TOP
X-RAY DIFFRACTION4ION.PARAMION.TOP

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