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- PDB-9jae: GMPK(S37P mutant) -

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Basic information

Entry
Database: PDB / ID: 9jae
TitleGMPK(S37P mutant)
ComponentsGuanylate kinase
KeywordsTRANSFERASE / guanylate kinase
Function / homology
Function and homology information


dATP metabolic process / dGDP biosynthetic process / GDP biosynthetic process / GDP-mannose metabolic process / guanylate kinase / purine nucleotide metabolic process / dGMP metabolic process / glycoprotein transport / GMP kinase activity / nucleobase-containing small molecule interconversion ...dATP metabolic process / dGDP biosynthetic process / GDP biosynthetic process / GDP-mannose metabolic process / guanylate kinase / purine nucleotide metabolic process / dGMP metabolic process / glycoprotein transport / GMP kinase activity / nucleobase-containing small molecule interconversion / Interconversion of nucleotide di- and triphosphates / Azathioprine ADME / photoreceptor inner segment / xenobiotic metabolic process / mitochondrion / ATP binding / cytosol
Similarity search - Function
Guanylate kinase / Guanylate kinase, conserved site / Guanylate kinase-like signature. / Guanylate kinase-like domain profile. / Guanylate kinase-like domain / Guanylate kinase/L-type calcium channel beta subunit / Guanylate kinase / Guanylate kinase homologues. / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 3 Å
AuthorsWang, L. / Ruan, K.
Funding support China, 3items
OrganizationGrant numberCountry
Ministry of Science and Technology (MoST, China)2019YFA0508400 China
National Natural Science Foundation of China (NSFC)22377119 China
Other privateYD9100002028 China
CitationJournal: Nat Commun / Year: 2025
Title: Comprehensive profiling of the catalytic conformations of human Guanylate kinase.
Authors: Wang, L. / Li, Z. / Xuan, Y. / Qin, J. / Li, S. / Zhong, F. / Song, Y. / Yang, K. / Lv, M. / Li, F. / Jiahai, Z. / Pan, Y. / Guang, S. / Zhao, Y. / Shi, Y. / Liu, X. / Du, Y. / Gao, J. / Ruan, K.
History
DepositionAug 24, 2024Deposition site: PDBJ / Processing site: PDBC
Revision 1.0Sep 3, 2025Provider: repository / Type: Initial release
Revision 1.1Sep 10, 2025Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Guanylate kinase
B: Guanylate kinase
C: Guanylate kinase
D: Guanylate kinase


Theoretical massNumber of molelcules
Total (without water)87,6074
Polymers87,6074
Non-polymers00
Water00
1
A: Guanylate kinase
C: Guanylate kinase


Theoretical massNumber of molelcules
Total (without water)43,8042
Polymers43,8042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1590 Å2
ΔGint-10 kcal/mol
Surface area19260 Å2
MethodPISA
2
B: Guanylate kinase

D: Guanylate kinase


Theoretical massNumber of molelcules
Total (without water)43,8042
Polymers43,8042
Non-polymers00
Water0
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_445x-1/2,y-1/2,z1
Buried area1500 Å2
ΔGint-10 kcal/mol
Surface area19590 Å2
MethodPISA
Unit cell
Length a, b, c (Å)82.777, 87.750, 198.474
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Guanylate kinase / GMP kinase / Guanylate kinase 1


Mass: 21901.768 Da / Num. of mol.: 4 / Mutation: S37P
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: GUK1, GMK, GMPK / Production host: Escherichia coli (E. coli) / References: UniProt: Q16774, guanylate kinase
Has protein modificationN

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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: 2.06 Å3/Da / Density % sol: 40.2 %
Crystal growTemperature: 277 K / Method: vapor diffusion, sitting drop / Details: 20% w/v PEG 3350, 0.2 M di-Ammonium Tartrate

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL19U1 / Wavelength: 0.97853 Å
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL / Date: Mar 19, 2023
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97853 Å / Relative weight: 1
ReflectionResolution: 3→33.14 Å / Num. obs: 14767 / % possible obs: 99.7 % / Redundancy: 4.3 % / CC1/2: 0.987 / Rmerge(I) obs: 0.171 / Rpim(I) all: 0.091 / Rrim(I) all: 0.194 / Χ2: 0.98 / Net I/σ(I): 6.7 / Num. measured all: 63422
Reflection shellResolution: 3→3.18 Å / % possible obs: 99.9 % / Redundancy: 4.4 % / Rmerge(I) obs: 0.521 / Num. measured all: 10308 / Num. unique obs: 2369 / CC1/2: 0.834 / Rpim(I) all: 0.279 / Rrim(I) all: 0.595 / Χ2: 0.94 / Net I/σ(I) obs: 2.6

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Processing

Software
NameVersionClassification
PHENIX(1.19_4092: ???)refinement
Aimlessdata scaling
XDSdata reduction
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 9J8L

9j8l


Resolution: 3→32.87 Å / SU ML: 0.36 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 31.72 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2821 715 4.85 %
Rwork0.2334 --
obs0.2358 14748 99.41 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 3→32.87 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5776 0 0 0 5776
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0025868
X-RAY DIFFRACTIONf_angle_d0.4257973
X-RAY DIFFRACTIONf_dihedral_angle_d3.477829
X-RAY DIFFRACTIONf_chiral_restr0.037928
X-RAY DIFFRACTIONf_plane_restr0.0041066
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
3-3.230.37641210.30772781X-RAY DIFFRACTION100
3.23-3.560.32171590.26452760X-RAY DIFFRACTION100
3.56-4.070.29951660.22772769X-RAY DIFFRACTION100
4.07-5.120.24291520.20972787X-RAY DIFFRACTION99
5.13-32.870.2331170.20912936X-RAY DIFFRACTION99
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)
10.57620.4835-0.00170.48780.20750.6856-0.1026-0.25420.05450.1647-0.0073-0.17080.1057-0.14530.02260.141-0.1965-0.06280.05590.13151.275946.9650.564624.4804
20.3925-0.25580.38690.70150.18411.69840.0719-0.0901-0.4153-0.0423-0.15640.17750.1815-0.1080.09750.1811-0.0656-0.02650.3057-0.03240.637439.4631-2.800219.8207
31.3272-0.19880.32560.63880.42121.5435-0.18690.1333-0.0511-0.10670.1460.36560.2856-0.11510.03040.3936-0.09550.01480.1939-0.05060.878339.5057-10.677410.6495
41.73320.3243-0.90890.1083-0.41662.5048-0.0246-0.0683-0.05450.1393-0.0162-0.0928-0.0027-0.0669-0.00140.1322-0.0202-0.03370.1952-0.01110.858619.165815.3416.8294
53.02753.31321.20553.67951.05221.51810.03190.02351.3030.274-0.37181.1314-0.37720.07750.29070.3497-0.0234-0.02820.45660.05451.047135.015533.30968.9697
61.8999-1.3720.97862.1194-0.26560.7031-0.02590.29230.403-0.3911-0.043-0.55950.09940.0857-0.02240.0761-0.11880.08870.3117-0.02530.091524.768619.1514-1.7236
72.2405-0.70132.24542.08931.04894.1656-0.1673-0.32290.07850.28240.6791-0.09090.31340.4057-0.31070.2797-0.078-0.00980.3416-0.16890.311623.9838-23.661243.382
81.02880.82650.44723.74332.32022.13270.0337-0.03760.03310.0168-0.23740.4795-0.4560.19480.09070.397-0.1798-0.12590.25490.16150.828914.8023-24.224427.6989
93.18222.9109-1.11152.6776-1.18953.1292-0.30720.215-0.8125-0.41890.06360.2026-0.18870.00230.21270.4182-0.0948-0.06820.3182-0.09370.948930.5995-8.029540.4452
103.26740.68380.96616.41190.21733.37060.2924-0.27320.66430.6952-0.45340.50960.36510.04050.1830.3206-0.07780.05840.3177-0.0620.464921.1718-18.945851.5073
111.0150.5058-1.42940.8511-0.32632.6224-0.11930.0983-0.2816-0.00960.0623-0.0430.4621-0.28110.0460.2782-0.070600.2385-0.01730.73441.23410.476827.2798
120.76551.41222.11382.86083.20887.7812-1.01360.04530.1250.1269-0.79140.9143-0.8079-1.43451.74820.56760.10510.03220.6254-0.11481.3498-24.6826-12.596329.6872
134.69460.50585.01770.24530.92897.7655-0.4990.35230.30980.0931-0.26120.1945-0.16640.08430.62820.2943-0.2368-0.05050.42630.12351.0054-14.1559-17.004531.5362
140.6445-0.9027-0.0653.34990.97551.9551-0.1337-0.2884-0.13610.6-0.4016-0.01810.077-0.1050.43420.392-0.1148-0.08690.36970.12410.9919-8.94511.591743.2235
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1chain 'D' and (resid 3 through 67 )
2X-RAY DIFFRACTION2chain 'D' and (resid 68 through 142 )
3X-RAY DIFFRACTION3chain 'D' and (resid 143 through 196 )
4X-RAY DIFFRACTION4chain 'A' and (resid 3 through 118 )
5X-RAY DIFFRACTION5chain 'A' and (resid 119 through 159 )
6X-RAY DIFFRACTION6chain 'A' and (resid 160 through 196 )
7X-RAY DIFFRACTION7chain 'B' and (resid 4 through 38 )
8X-RAY DIFFRACTION8chain 'B' and (resid 39 through 113 )
9X-RAY DIFFRACTION9chain 'B' and (resid 114 through 161 )
10X-RAY DIFFRACTION10chain 'B' and (resid 162 through 196 )
11X-RAY DIFFRACTION11chain 'C' and (resid 3 through 127 )
12X-RAY DIFFRACTION12chain 'C' and (resid 128 through 143 )
13X-RAY DIFFRACTION13chain 'C' and (resid 144 through 161 )
14X-RAY DIFFRACTION14chain 'C' and (resid 162 through 195 )

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