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- PDB-2ako: Crystal structure of Glutamate 5-kinase from Campylobacter jejuni -

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Basic information

Entry
Database: PDB / ID: 2ako
TitleCrystal structure of Glutamate 5-kinase from Campylobacter jejuni
ComponentsGlutamate 5-kinase
KeywordsTRANSFERASE / Structural Genomics / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics / NYSGXRC
Function / homology
Function and homology information


glutamate 5-kinase / glutamate 5-kinase activity / L-proline biosynthetic process / ATP binding / cytoplasm
Similarity search - Function
Glutamate 5-kinase / Glutamate-5-kinase domain / Glutamate 5-kinase/delta-1-pyrroline-5-carboxylate synthase / Glutamate 5-kinase, conserved site / Glutamate 5-kinase signature. / Glutamate/acetylglutamate kinase / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Amino acid kinase family ...Glutamate 5-kinase / Glutamate-5-kinase domain / Glutamate 5-kinase/delta-1-pyrroline-5-carboxylate synthase / Glutamate 5-kinase, conserved site / Glutamate 5-kinase signature. / Glutamate/acetylglutamate kinase / Carbamate kinase / Acetylglutamate kinase-like / Aspartate/glutamate/uridylate kinase / Amino acid kinase family / Acetylglutamate kinase-like superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Glutamate 5-kinase
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsGorman, J. / Shapiro, L. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of Glutamate 5-kinase from Campylobacter jejuni
Authors: Gorman, J. / Shapiro, L.
History
DepositionAug 3, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 9, 2005Provider: 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: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn ...audit_author / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag ..._audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _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

Downloads & links

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Assembly

Deposited unit
A: Glutamate 5-kinase
B: Glutamate 5-kinase
C: Glutamate 5-kinase
D: Glutamate 5-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)114,1728
Polymers112,4634
Non-polymers1,7094
Water12,827712
1
A: Glutamate 5-kinase
B: Glutamate 5-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0864
Polymers56,2312
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4470 Å2
ΔGint-41 kcal/mol
Surface area20030 Å2
MethodPISA
2
C: Glutamate 5-kinase
D: Glutamate 5-kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,0864
Polymers56,2312
Non-polymers8542
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4380 Å2
ΔGint-40 kcal/mol
Surface area20160 Å2
MethodPISA
Unit cell
Length a, b, c (Å)98.597, 99.409, 124.547
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein
Glutamate 5-kinase / / Gamma-glutamyl kinase / GK


Mass: 28115.740 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: proB / Plasmid: Modified pET / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q9PJ29, glutamate 5-kinase
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


Mass: 427.201 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 712 / 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: 2.59 Å3/Da / Density % sol: 52.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: 23% PEG 3350, .1M Hepes 7.5, .2M NaMalonate, Cryo 30% sucrose, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9791 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 17, 2005
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.2→20 Å / Num. all: 59989 / Num. obs: 59989 / % possible obs: 96.1 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Rmerge(I) obs: 0.103 / Net I/σ(I): 10.4
Reflection shellResolution: 2.2→2.28 Å / Redundancy: 3 % / Rmerge(I) obs: 0.326 / Mean I/σ(I) obs: 3.2 / Num. unique all: 5524 / % possible all: 89.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: SAD / Resolution: 2.2→20 Å / Cor.coef. Fo:Fc: 0.95 / Cor.coef. Fo:Fc free: 0.926 / SU B: 5.152 / SU ML: 0.132 / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): -3 / ESU R: 0.243 / ESU R Free: 0.193 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2213 3043 5.1 %RANDOM
Rwork0.17777 ---
all0.18005 59953 --
obs0.18005 59953 95.71 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 23.856 Å2
Baniso -1Baniso -2Baniso -3
1--0.62 Å20 Å20 Å2
2---0.85 Å20 Å2
3---1.46 Å2
Refinement stepCycle: LAST / Resolution: 2.2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7570 0 135 712 8417
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0227833
X-RAY DIFFRACTIONr_bond_other_d0.0010.027284
X-RAY DIFFRACTIONr_angle_refined_deg1.2081.99110567
X-RAY DIFFRACTIONr_angle_other_deg0.741317003
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9925958
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.84225.415325
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.45151473
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.1931520
X-RAY DIFFRACTIONr_chiral_restr0.0650.21237
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028429
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021498
X-RAY DIFFRACTIONr_nbd_refined0.2010.21541
X-RAY DIFFRACTIONr_nbd_other0.1690.27078
X-RAY DIFFRACTIONr_nbtor_refined0.1730.23732
X-RAY DIFFRACTIONr_nbtor_other0.0810.24430
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2653
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.213
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2560.261
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1260.214
X-RAY DIFFRACTIONr_mcbond_it0.8411.56010
X-RAY DIFFRACTIONr_mcbond_other0.1131.51986
X-RAY DIFFRACTIONr_mcangle_it1.01427659
X-RAY DIFFRACTIONr_scbond_it1.57633465
X-RAY DIFFRACTIONr_scangle_it2.2244.52908
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.253 185 -
Rwork0.211 3444 -
obs--80.11 %

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