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- PDB-2x4g: Crystal structure of PA4631, a nucleoside-diphosphate-sugar epime... -

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Basic information

Entry
Database: PDB / ID: 2x4g
TitleCrystal structure of PA4631, a nucleoside-diphosphate-sugar epimerase from Pseudomonas aeruginosa
ComponentsNUCLEOSIDE-DIPHOSPHATE-SUGAR EPIMERASE
KeywordsISOMERASE
Function / homology
Function and homology information


aldehyde dehydrogenase (NAD+) activity / cytoplasm
Similarity search - Function
: / NAD-dependent epimerase/dehydratase / NAD dependent epimerase/dehydratase family / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NAD-dependent epimerase/dehydratase domain-containing protein
Similarity search - Component
Biological speciesPSEUDOMONAS AERUGINOSA (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.65 Å
AuthorsOke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / White, M.F. / Naismith, J.H.
CitationJournal: J.Struct.Funct.Genomics / Year: 2010
Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs.
Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili, D. / Botting, C.H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H.
History
DepositionJan 30, 2010Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jul 21, 2010Provider: repository / Type: Initial release
Revision 1.1May 7, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jan 24, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: NUCLEOSIDE-DIPHOSPHATE-SUGAR EPIMERASE


Theoretical massNumber of molelcules
Total (without water)37,3671
Polymers37,3671
Non-polymers00
Water75742
1
A: NUCLEOSIDE-DIPHOSPHATE-SUGAR EPIMERASE

A: NUCLEOSIDE-DIPHOSPHATE-SUGAR EPIMERASE


Theoretical massNumber of molelcules
Total (without water)74,7332
Polymers74,7332
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_656-x+y+1,y,-z+11
Buried area1930 Å2
ΔGint-22.1 kcal/mol
Surface area27050 Å2
MethodPISA
Unit cell
Length a, b, c (Å)83.380, 83.380, 215.720
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number180
Space group name H-MP6222

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Components

#1: Protein NUCLEOSIDE-DIPHOSPHATE-SUGAR EPIMERASE


Mass: 37366.730 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) PSEUDOMONAS AERUGINOSA (bacteria) / Strain: PAO1 / Plasmid: PDEST14 / Production host: ESCHERICHIA COLI BL21(DE3) (bacteria) / Variant (production host): C43 / References: UniProt: Q9HVG0
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / 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: 2.91 Å3/Da / Density % sol: 57.7 % / Description: NONE
Crystal growpH: 8
Details: 2.55M NACL, 0.1M HEPES PH 8 OR 2.9M NACL, 0.1M BICINE PH 8.5 AT A PROTEIN CONCENTRATION OF 2 MG ML-1.CRYSTALS WERE CRYOPROTECTED DIRECTLY IN THIS SOLUTION SUPPLEMENTED WITH 18% GLYCEROL. ...Details: 2.55M NACL, 0.1M HEPES PH 8 OR 2.9M NACL, 0.1M BICINE PH 8.5 AT A PROTEIN CONCENTRATION OF 2 MG ML-1.CRYSTALS WERE CRYOPROTECTED DIRECTLY IN THIS SOLUTION SUPPLEMENTED WITH 18% GLYCEROL. CRYSTAL WAS SOAKED IN 20MM TRIMETHYLLEADCHLORIDE FOR APPROXIMATELY 5 MINUTES BEFORE BEING BACK SOAKED IN CRYO BUFFER

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-4 / Wavelength: 0.939
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 21, 2008 / Details: MIRRORS
RadiationMonochromator: SI(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.939 Å / Relative weight: 1
ReflectionResolution: 2.65→41.7 Å / Num. obs: 12600 / % possible obs: 97 % / Observed criterion σ(I): 0 / Redundancy: 5 % / Rmerge(I) obs: 0.08 / Net I/σ(I): 23.3
Reflection shellResolution: 2.65→2.7 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.66 / Mean I/σ(I) obs: 2.75 / % possible all: 90

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Processing

Software
NameVersionClassification
REFMAC5.5.0070refinement
XDSdata reduction
SCALEPACKdata scaling
SHELXCDESOLVE RESOLVEphasing
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.65→41.7 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.908 / SU B: 23.747 / SU ML: 0.216 / Cross valid method: THROUGHOUT / ESU R: 0.49 / ESU R Free: 0.297 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE STRUCTURE IS ORDERED FROM RESIDUES 11 TO 83, 96 TO 280 AND 297 TO 340. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU ...Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. THE STRUCTURE IS ORDERED FROM RESIDUES 11 TO 83, 96 TO 280 AND 297 TO 340. ATOM RECORD CONTAINS SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORD CONTAINS SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflectionSelection details
Rfree0.25314 679 5.1 %RANDOM
Rwork0.21142 ---
obs0.21346 12600 97 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 30.888 Å2
Baniso -1Baniso -2Baniso -3
1-0.92 Å20.46 Å20 Å2
2--0.92 Å20 Å2
3----1.39 Å2
Refinement stepCycle: LAST / Resolution: 2.65→41.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2301 0 0 42 2343
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0212344
X-RAY DIFFRACTIONr_bond_other_d0.0010.021612
X-RAY DIFFRACTIONr_angle_refined_deg1.3321.9713169
X-RAY DIFFRACTIONr_angle_other_deg0.84533886
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3195299
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.40122.264106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.63515382
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.6311526
X-RAY DIFFRACTIONr_chiral_restr0.070.2349
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0212653
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02499
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5641.51487
X-RAY DIFFRACTIONr_mcbond_other0.0781.5623
X-RAY DIFFRACTIONr_mcangle_it1.11122350
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.6913857
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.9454.5819
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.648→2.716 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.4 51 -
Rwork0.387 822 -
obs--90.09 %
Refinement TLS params.Method: refined / Origin x: 25.5009 Å / Origin y: 9.3698 Å / Origin z: 126.2196 Å
111213212223313233
T0.1309 Å20.0521 Å2-0.0072 Å2-0.0783 Å2-0.0608 Å2--0.0783 Å2
L1.2212 °20.3338 °2-0.0037 °2-1.5707 °2-0.156 °2--1.0858 °2
S-0.0686 Å °0.1457 Å °-0.0627 Å °-0.189 Å °-0.0599 Å °-0.0075 Å °0.0414 Å °-0.0888 Å °0.1286 Å °

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