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- PDB-2p5y: Crystal structure of Thermus thermophilus HB8 UDP-glucose 4-epime... -

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Basic information

Entry
Database: PDB / ID: 2p5y
TitleCrystal structure of Thermus thermophilus HB8 UDP-glucose 4-epimerase complex with NAD
ComponentsUDP-glucose 4-epimerase
KeywordsISOMERASE / TTHA0591 / STRUCTURAL GENOMICS / UDP-glucose 4-epimerase / Thermus thermophilus HB8 / PSI / Protein Structure Initiative / Southeast Collaboratory for Structural Genomics / SECSG / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN STRUCTURAL GENOMICS/PROTEOMICS INITIATIVE / RSGI
Function / homology
Function and homology information


UDP-galactose 4-epimerase, domain 1 / UDP-galactose 4-epimerase; domain 1 / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / UDP-glucose 4-epimerase
Similarity search - Component
Biological speciesThermus thermophilus HB8 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.92 Å
AuthorsFu, Z.-Q. / Chen, L. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Zhu, J. / Swindell, J.T. / Chrzas, J. / Rose, J.P. ...Fu, Z.-Q. / Chen, L. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Zhu, J. / Swindell, J.T. / Chrzas, J. / Rose, J.P. / Wang, B.-C. / Southeast Collaboratory for Structural Genomics (SECSG) / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of Thermus thermophilus HB8 UDP-glucose 4-epimerase complex with NAD
Authors: Fu, Z.-Q. / Chen, L. / Ebihara, A. / Shinkai, A. / Kuramitsu, S. / Yokoyama, S. / Zhu, J. / Swindell, J.T. / Chrzas, J. / Rose, J.P. / Wang, B.-C.
History
DepositionMar 16, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 17, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version
Revision 1.4Jan 24, 2018Group: Database references / Structure summary / Category: audit_author / citation_author / Item: _audit_author.name / _citation_author.name
Revision 1.5Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300 BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 ... BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 1 CHAIN(S). AUTHORS STATE THAT THE BIOLOGICAL UNIT OF THIS PROTEIN IS A MONOMER.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: UDP-glucose 4-epimerase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)34,4802
Polymers33,8161
Non-polymers6631
Water3,909217
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)135.667, 135.667, 135.667
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number213
Space group name H-MP4132
DetailsThe biological assembly is a monomer with NAD

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Components

#1: Protein UDP-glucose 4-epimerase /


Mass: 33816.395 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus HB8 (bacteria) / Species: Thermus thermophilus / Strain: HB8, DSM 579 / Gene: TTHA0591 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SKQ2, UDP-glucose 4-epimerase
#2: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Nicotinamide adenine dinucleotide


Mass: 663.425 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 217 / 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: 3.07 Å3/Da / Density % sol: 60 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 5.6
Details: USING 1 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (11.71 mg/ml) AND RESERVOIR SOLUTION CONTAINING 1.0M Magnesium sulfate, 0.1M Sodium citrate, pH 5.6, VAPOR DIFFUSION, ...Details: USING 1 MICROLITER DROPS CONTAINING EQUAL VOLUMES OF PROTEIN CONCENTRATE (11.71 mg/ml) AND RESERVOIR SOLUTION CONTAINING 1.0M Magnesium sulfate, 0.1M Sodium citrate, pH 5.6, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-BM / Wavelength: 0.97928 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 1, 2007 / Details: mirrors
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97928 Å / Relative weight: 1
ReflectionRedundancy: 42.4 % / Av σ(I) over netI: 15.2 / Number: 1405343 / Rmerge(I) obs: 0.068 / Χ2: 1.55 / D res high: 1.92 Å / D res low: 50 Å / Num. obs: 33164 / % possible obs: 100
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsChi squaredRedundancy
4.145099.910.0463.04538.4
3.284.1410010.0583.32741.3
2.873.2810010.062.04842.8
2.612.8710010.0711.50743.3
2.422.6110010.0861.23843.4
2.282.4210010.1051.05543.5
2.162.2810010.1370.93843.5
2.072.1610010.1710.85743.4
1.992.0710010.2390.76843.2
1.921.9910010.3120.71341.4
ReflectionResolution: 1.92→50 Å / Num. all: 33164 / Num. obs: 33164 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 42.4 % / Rsym value: 0.068 / Χ2: 1.549 / Net I/σ(I): 15.2
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsNum. unique allΧ2% possible all
1.92-1.9941.40.31232300.713100
1.99-2.0743.20.23932440.768100
2.07-2.1643.40.17132490.857100
2.16-2.2843.50.13732630.938100
2.28-2.4243.50.10532831.055100
2.42-2.6143.40.08632771.238100
2.61-2.8743.30.07133081.507100
2.87-3.2842.80.0633192.048100
3.28-4.1441.30.05833853.327100
4.14-5038.40.04636063.04599.9

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.2.0019refinement
PDB_EXTRACT2data extraction
SERGUIdata collection
HKL-2000data reduction
EPMRphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2P5U

2p5u


Resolution: 1.92→30 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.939 / SU B: 2.298 / SU ML: 0.069 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.133 / ESU R Free: 0.118 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.207 1673 5.1 %RANDOM
Rwork0.191 ---
obs0.192 33064 99.95 %-
all-33064 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.125 Å2
Refinement stepCycle: LAST / Resolution: 1.92→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2387 0 44 217 2648
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0222493
X-RAY DIFFRACTIONr_angle_refined_deg1.2821.993393
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3355310
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.20722.727110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.56415382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg15.5441522
X-RAY DIFFRACTIONr_chiral_restr0.0850.2367
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021923
X-RAY DIFFRACTIONr_nbd_refined0.1880.21193
X-RAY DIFFRACTIONr_nbtor_refined0.3060.21687
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1410.2214
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1680.237
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1120.213
X-RAY DIFFRACTIONr_mcbond_it0.891.51583
X-RAY DIFFRACTIONr_mcangle_it1.34322462
X-RAY DIFFRACTIONr_scbond_it2.19331028
X-RAY DIFFRACTIONr_scangle_it3.5574.5931
LS refinement shellResolution: 1.92→1.971 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.252 132 -
Rwork0.189 2260 -
obs-2392 100 %

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