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- PDB-2b8n: Crystal structure of Glycerate kinase (EC 2.7.1.31) (tm1585) from... -

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Basic information

Entry
Database: PDB / ID: 2b8n
TitleCrystal structure of Glycerate kinase (EC 2.7.1.31) (tm1585) from THERMOTOGA MARITIMA at 2.70 A resolution
Componentsglycerate kinase, putative
KeywordsTRANSFERASE / tm1585 / Glycerate kinase (EC 2.7.1.31) / Structural Genomics / Joint Center for Structural Genomics / JCSG / Protein Structure Initiative / PSI
Function / homology
Function and homology information


glycerate 2-kinase / glycerate 2-kinase activity / glycerate kinase activity / phosphotransferase activity, alcohol group as acceptor / magnesium ion binding / ATP binding / cytoplasm
Similarity search - Function
glycerate kinase, domain 1 / MOFRL domain / Glycerate kinase, MOFRL-like N-terminal domain / MOFRL domain / MOFRL-associated domain / Glycerate kinase-like, C-terminal domain superfamily / Glycerate kinase, N-terminal domain superfamily / MOFRL domain-containing protein / MOFRL family / Domain of unknown function (DUF4147) ...glycerate kinase, domain 1 / MOFRL domain / Glycerate kinase, MOFRL-like N-terminal domain / MOFRL domain / MOFRL-associated domain / Glycerate kinase-like, C-terminal domain superfamily / Glycerate kinase, N-terminal domain superfamily / MOFRL domain-containing protein / MOFRL family / Domain of unknown function (DUF4147) / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
D-glycerate 2-kinase
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.53 Å
AuthorsJoint Center for Structural Genomics (JCSG)
CitationJournal: Proteins / Year: 2006
Title: Crystal structure of a glycerate kinase (TM1585) from Thermotoga maritima at 2.70 A resolution reveals a new fold
Authors: Schwarzenbacher, R. / McMullan, D. / Krishna, S.S. / Xu, Q. / Miller, M.D. / Canaves, J.M. / Elsliger, M.A. / Floyd, R. / Grzechnik, S.K. / Jaroszewski, L. / Klock, H.E. / Koesema, E. / ...Authors: Schwarzenbacher, R. / McMullan, D. / Krishna, S.S. / Xu, Q. / Miller, M.D. / Canaves, J.M. / Elsliger, M.A. / Floyd, R. / Grzechnik, S.K. / Jaroszewski, L. / Klock, H.E. / Koesema, E. / Kovarik, J.S. / Kreusch, A. / Kuhn, P. / McPhillips, T.M. / Morse, A.T. / Quijano, K. / Spraggon, G. / Stevens, R.C. / van den Bedem, H. / Wolf, G. / Hodgson, K.O. / Wooley, J. / Deacon, A.M. / Godzik, A. / Lesley, S.A. / Wilson, I.A.
History
DepositionOct 7, 2005Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 8, 2005Provider: repository / Type: Initial release
SupersessionMar 28, 2006ID: 1O0U
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Source and taxonomy / Version format compliance
Revision 1.3Jan 25, 2023Group: Database references / Derived calculations / Category: database_2 / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Oct 30, 2024Group: Data collection / Refinement description / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / pdbx_entry_details / pdbx_modification_feature / struct_ncs_dom_lim
Item: _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.end_auth_comp_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: glycerate kinase, putative
B: glycerate kinase, putative


Theoretical massNumber of molelcules
Total (without water)92,9532
Polymers92,9532
Non-polymers00
Water1,74797
1
A: glycerate kinase, putative


Theoretical massNumber of molelcules
Total (without water)46,4761
Polymers46,4761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: glycerate kinase, putative


Theoretical massNumber of molelcules
Total (without water)46,4761
Polymers46,4761
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)61.954, 85.169, 172.507
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31A
41B
51A
61B
71A
81B
91A
101B
111A
121B
131A
141B
12A
22B
32A
42B
52A
62B
72A
82B
92A
102B
112A
122B
132A
142B
152A
162B
172A
182B
192A
202B
212A
222B

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDRefine codeAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111PROPROGLUGLU5AA4 - 516 - 17
211PROPROGLUGLU5BB4 - 516 - 17
321SERSERPHEPHE2AA6 - 2318 - 35
421SERSERPHEPHE2BB6 - 2318 - 35
531GLYGLYLYSLYS2AA249 - 263261 - 275
631GLYGLYLYSLYS2BB249 - 263261 - 275
741GLUGLUGLUGLU3AA264276
841GLUGLUGLUGLU3BB264276
951LYSLYSILEILE2AA265 - 340277 - 352
1051LYSLYSILEILE2BB265 - 340277 - 352
1161GLUGLUGLUGLU3AA341353
1261GLUGLUGLUGLU3BB341353
1371GLYGLYVALVAL2AA342 - 417354 - 429
1471GLYGLYVALVAL2BB342 - 417354 - 429
112PROPROLEULEU2AA24 - 3736 - 49
212PROPROLEULEU2BB24 - 3736 - 49
322ASPASPASPASP3AA3850
422ASPASPASPASP3BB3850
532ARGARGTRPTRP2AA39 - 5051 - 62
632ARGARGTRPTRP2BB39 - 5051 - 62
742ARGARGARGARG3AA5163
842ARGARGARGARG3BB5163
952MSEMSEGLYGLY2AA52 - 6164 - 73
1052MSEMSEGLYGLY2BB52 - 6164 - 73
1162LYSLYSLYSLYS3AA6274
1262LYSLYSLYSLYS3BB6274
1372LYSLYSASNASN2AA63 - 11275 - 124
1472LYSLYSASNASN2BB63 - 11275 - 124
1582GLUGLUASNASN3AA113 - 114125 - 126
1682GLUGLUASNASN3BB113 - 114125 - 126
1792ASPASPLEULEU2AA115 - 149127 - 161
1892ASPASPLEULEU2BB115 - 149127 - 161
19102LYSLYSLYSLYS3AA150162
20102LYSLYSLYSLYS3BB150162
21112SERSERILEILE2AA151 - 248163 - 260
22112SERSERILEILE2BB151 - 248163 - 260

NCS ensembles :
ID
1
2

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Components

#1: Protein glycerate kinase, putative


Mass: 46476.414 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Strain: MSB8 / Gene: tm1585 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9X1S1, glycerate 3-kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 97 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.6 Å3/Da / Density % sol: 52.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop, nanodrop / pH: 9
Details: 65% MPD, 0.1M bicine pH 9.0 , VAPOR DIFFUSION,SITTING DROP,NANODROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.904965, 0.979126
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 7, 2002
RadiationMonochromator: DOUBLE CRYSTAL MONOCHROMATOR / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9049651
20.9791261
ReflectionResolution: 2.52→48.11 Å / Num. obs: 26442 / % possible obs: 75.1 % / Redundancy: 2.89 % / Rmerge(I) obs: 0.072 / Rsym value: 0.072 / Net I/σ(I): 7.71
Reflection shell

Diffraction-ID: 1

Resolution (Å)% possible obs (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. unique obsRsym value
2.52-2.6130.20.2342.59252217870.234
2.61-2.7141.30.3152.9235962373
2.71-2.8450.70.3153.5452843206
2.84-2.9966.40.3154.0668623934
2.99-3.1790.90.3154.9291845231
3.17-3.4294.20.3156.2799765762
3.42-3.7694.40.3158.495875548
3.76-4.394.60.3159.9997205624
4.3-5.494.80.31512.0696815625
5.4-48.1193.20.31512.9699755685

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0005refinement
XSCALEdata scaling
PDB_EXTRACT1.601data extraction
XDSdata reduction
SHELXphasing
autoSHARPphasing
RefinementMethod to determine structure: MAD / Resolution: 2.53→48.11 Å / Cor.coef. Fo:Fc: 0.94 / Cor.coef. Fo:Fc free: 0.897 / SU B: 19.801 / SU ML: 0.206 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 3.762 / ESU R Free: 0.334
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE NOMINAL RESOLUTION IS 2.70 A WITH 2890 OBSERVED REFLECTIONS BETWEEN 2.70-2.53 (52.8% COMPLETE FOR THIS SHELL) INCLUDED IN THE REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.246 1314 5 %RANDOM
Rwork0.182 ---
all0.185 ---
obs0.1848 25084 84.37 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 27.296 Å2
Baniso -1Baniso -2Baniso -3
1--0.29 Å20 Å20 Å2
2---1.01 Å20 Å2
3---1.3 Å2
Refinement stepCycle: LAST / Resolution: 2.53→48.11 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6147 0 0 97 6244
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226228
X-RAY DIFFRACTIONr_bond_other_d0.0010.025951
X-RAY DIFFRACTIONr_angle_refined_deg1.3791.9918424
X-RAY DIFFRACTIONr_angle_other_deg0.821313856
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8555826
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.93625.312224
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.219151124
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.3431529
X-RAY DIFFRACTIONr_chiral_restr0.0720.21014
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.026893
X-RAY DIFFRACTIONr_gen_planes_other0.0020.021104
X-RAY DIFFRACTIONr_nbd_refined0.2070.21255
X-RAY DIFFRACTIONr_nbd_other0.1690.25752
X-RAY DIFFRACTIONr_nbtor_refined0.170.23032
X-RAY DIFFRACTIONr_nbtor_other0.0830.23883
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.160.2186
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3160.29
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2480.236
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1190.22
X-RAY DIFFRACTIONr_mcbond_it1.1834237
X-RAY DIFFRACTIONr_mcbond_other0.37931704
X-RAY DIFFRACTIONr_mcangle_it1.83456562
X-RAY DIFFRACTIONr_scbond_it3.82882252
X-RAY DIFFRACTIONr_scangle_it5.613111862
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Refine-ID: X-RAY DIFFRACTION

Ens-IDNumberTypeRms dev position (Å)Weight position
11095TIGHT POSITIONAL0.040.05
11519MEDIUM POSITIONAL0.280.5
138LOOSE POSITIONAL0.825
11095TIGHT THERMAL0.110.5
11519MEDIUM THERMAL0.612
138LOOSE THERMAL2.1410
21324TIGHT POSITIONAL0.040.05
21959MEDIUM POSITIONAL0.240.5
261LOOSE POSITIONAL1.455
21324TIGHT THERMAL0.10.5
21959MEDIUM THERMAL0.592
261LOOSE THERMAL2.2510
LS refinement shellResolution: 2.53→2.596 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 51 -
Rwork0.24 1055 -
obs--48.19 %
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)
12.61190.5724-0.482.1002-0.17012.30070.192-0.04770.19550.0194-0.15120.4779-0.2273-0.1552-0.0408-0.12480.0255-0.0156-0.1074-0.0446-0.050455.516246.121160.8785
22.1903-0.45550.99721.9848-0.28862.1402-0.0474-0.10640.01490.12270.01680.06740.0715-0.02760.0306-0.0612-0.0204-0.0119-0.1093-0.0559-0.076650.32612.613965.5688
32.48980.15820.41232.66890.19272.09050.0683-0.0608-0.03480.0888-0.0568-0.32120.08830.1629-0.0115-0.12850.0165-0.029-0.11160.0086-0.125680.873539.883661.2018
42.55030.0709-0.29831.79571.01332.172-0.1775-0.0779-0.00220.11140.0494-0.1398-0.0099-0.05420.1282-0.0078-0.0523-0.0854-0.0553-0.03520.017385.461973.114167.5128
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Selection: all

IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11AA4 - 2316 - 35
21AA249 - 417261 - 429
32AA24 - 24836 - 260
43BB4 - 2316 - 35
53BB249 - 417261 - 429
64BB24 - 24836 - 260

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