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- PDB-3oh8: Crystal structure of the nucleoside-diphosphate sugar epimerase f... -

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Basic information

Entry
Database: PDB / ID: 3oh8
TitleCrystal structure of the nucleoside-diphosphate sugar epimerase from Corynebacterium glutamicum. Northeast Structural Genomics Consortium Target CgR91
ComponentsNucleoside-diphosphate sugar epimerase (SulA family)
KeywordsISOMERASE / DUF1731_C / Northeast Structural Genomics Consortium / NESG / CgR91 / PSI-Biology / Protein Structure Initiative
Function / homologySTART domain / Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 4 / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta / :
Function and homology information
Biological speciesCorynebacterium glutamicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.997 Å
AuthorsVorobiev, S. / Lew, S. / Kuzin, A. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. ...Vorobiev, S. / Lew, S. / Kuzin, A. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F. / Northeast Structural Genomics Consortium (NESG)
CitationJournal: To be Published
Title: Crystal structure of the nucleoside-diphosphate sugar epimerase from Corynebacterium glutamicum. Northeast Structural Genomics Consortium Target CgR91.
Authors: Vorobiev, S. / Lew, S. / Kuzin, A. / Mao, M. / Xiao, R. / Ciccosanti, C. / Wang, H. / Everett, J.K. / Nair, R. / Acton, T.B. / Rost, B. / Montelione, G.T. / Tong, L. / Hunt, J.F.
History
DepositionAug 17, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 1, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 22, 2012Group: Structure summary
Revision 1.3Nov 8, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Nucleoside-diphosphate sugar epimerase (SulA family)


Theoretical massNumber of molelcules
Total (without water)56,9741
Polymers56,9741
Non-polymers00
Water5,495305
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)64.497, 74.083, 128.440
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Nucleoside-diphosphate sugar epimerase (SulA family)


Mass: 56974.203 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Corynebacterium glutamicum (bacteria) / Gene: cg1819 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)+ Magic / References: UniProt: Q6M4Z6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 305 / 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: 2.69 Å3/Da / Density % sol: 54.32 %
Crystal growTemperature: 278 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2% PEG 20000, 0.1M magnesium acetate, 0.1M sodium acetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 278K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X4A / Wavelength: 0.97901 Å
DetectorType: ADSC QUANTUM 4r / Detector: CCD / Date: Aug 10, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97901 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. all: 80580 / Num. obs: 73892 / % possible obs: 91.7 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.2 % / Biso Wilson estimate: 23.1 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 22.03
Reflection shellResolution: 2→2.07 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.508 / Mean I/σ(I) obs: 3.8 / Num. unique all: 8059 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
PHENIX1.6_289refinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
HKL-2000data reduction
HKL-2000data scaling
SnBphasing
RefinementMethod to determine structure: SAD / Resolution: 1.997→38.776 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.26 / Cross valid method: THROUGHOUT / σ(F): 1.03 / Phase error: 21.56 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.22 3556 5 %RANDOM
Rwork0.188 ---
obs0.19 71080 88.07 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 40.556 Å2 / ksol: 0.331 e/Å3
Displacement parametersBiso max: 127.27 Å2 / Biso mean: 28.939 Å2 / Biso min: 7.75 Å2
Baniso -1Baniso -2Baniso -3
1-6.956 Å2-0 Å2-0 Å2
2---0.478 Å2-0 Å2
3----6.478 Å2
Refinement stepCycle: LAST / Resolution: 1.997→38.776 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3488 0 0 305 3793
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.013563
X-RAY DIFFRACTIONf_angle_d1.0554846
X-RAY DIFFRACTIONf_chiral_restr0.071554
X-RAY DIFFRACTIONf_plane_restr0.004633
X-RAY DIFFRACTIONf_dihedral_angle_d16.0141263
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 24

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
1.997-2.0240.251730.2132879305294
2.024-2.0530.2281340.19830493183100
2.053-2.0840.2311410.20431033244100
2.084-2.1160.2411680.19430293197100
2.116-2.1510.2471570.19330973254100
2.151-2.1880.2311800.1830203200100
2.188-2.2280.262590.21388994835
2.27-2.3170.253810.2061747182875
2.317-2.3670.2371660.18330363202100
2.367-2.4220.2211350.18730653200100
2.422-2.4830.2451510.18331153266100
2.483-2.550.2261730.18930243197100
2.55-2.6250.2421620.19330513213100
2.625-2.710.2741550.19930753230100
2.71-2.8060.2541670.19831113278100
2.806-2.9190.2221770.18530193196100
2.919-3.0520.1821510.17430773228100
3.052-3.2120.1941770.18530653242100
3.212-3.4140.2181720.1930203192100
3.414-3.6770.249940.1931817191187
3.677-4.0470.1781140.1722031214577
4.047-4.6310.161520.15730823234100
4.631-5.8320.1931580.16230603218100
5.832-38.7840.2221590.19930633222100
Refinement TLS params.Method: refined / Origin x: 54.671 Å / Origin y: 27.233 Å / Origin z: 38.9902 Å
111213212223313233
T0.0156 Å2-0.0032 Å20.0082 Å2-0.025 Å20.0067 Å2--0.0287 Å2
L0.0781 °2-0.0652 °2-0.0703 °2-0.3216 °2-0.0386 °2--0.1611 °2
S-0.0054 Å °-0.0211 Å °-0.01 Å °-0.0057 Å °0.0137 Å °0.0192 Å °0.0539 Å °-0.021 Å °0 Å °
Refinement TLS groupSelection details: chain A

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