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- PDB-3e03: Crystal structure of a putative dehydrogenase from Xanthomonas ca... -

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Basic information

Entry
Database: PDB / ID: 3000
TitleCrystal structure of a putative dehydrogenase from Xanthomonas campestris
ComponentsShort chain dehydrogenase
KeywordsOXIDOREDUCTASE / STRUCTURAL GENOMICS / PSI-2 / DEHYDROGENASE / PROTEIN STRUCTURE INITIATIVE / NEW YORK STRUCTURAL GENOMIX RESEARCH CONSORTIUM / NYSGXRC / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


: / short chain dehydrogenase / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Short chain dehydrogenase
Similarity search - Component
Biological speciesXanthomonas campestris pv. campestris (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / Resolution: 1.69 Å
AuthorsSampathkumar, P. / Wasserman, S. / Rutter, M. / Hu, S. / Bain, K. / Rodgers, L. / Atwell, S. / Sauder, J.M. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal structure of a putative dehydrogenase from Xanthomonas campestris
Authors: Sampathkumar, P. / Wasserman, S. / Rutter, M. / Hu, S. / Bain, K. / Rodgers, L. / Atwell, S. / Sauder, J.M. / Burley, S.K.
History
DepositionJul 30, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 14, 2018Group: Data collection / Structure summary / Category: audit_author / Item: _audit_author.identifier_ORCID
Revision 1.3Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Oct 30, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Short chain dehydrogenase
B: Short chain dehydrogenase
C: Short chain dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,1044
Polymers86,0643
Non-polymers401
Water14,520806
1
A: Short chain dehydrogenase
hetero molecules

C: Short chain dehydrogenase


Theoretical massNumber of molelcules
Total (without water)57,4163
Polymers57,3762
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_554x,y,z-11
Buried area3120 Å2
ΔGint-39 kcal/mol
Surface area20130 Å2
MethodPISA
2
B: Short chain dehydrogenase

B: Short chain dehydrogenase


Theoretical massNumber of molelcules
Total (without water)57,3762
Polymers57,3762
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_656-x+1,y,-z+11
Buried area3030 Å2
ΔGint-32 kcal/mol
Surface area19710 Å2
MethodPISA
3
C: Short chain dehydrogenase

A: Short chain dehydrogenase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)57,4163
Polymers57,3762
Non-polymers401
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_556x,y,z+11
Unit cell
Length a, b, c (Å)251.286, 41.351, 73.323
Angle α, β, γ (deg.)90.000, 96.620, 90.000
Int Tables number5
Space group name H-MC121

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Components

#1: Protein Short chain dehydrogenase


Mass: 28687.979 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Xanthomonas campestris pv. campestris (bacteria)
Gene: XCC3285 / Plasmid: pSGX3(BC), modified pET26 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)-Codon+RIL / References: UniProt: Q8P5Q1
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 806 / 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: 2.2 Å3/Da / Density % sol: 44.05 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 100mM HEPES pH 7.5, 0.2M Calciumchloride,10% PEG 8000, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 31-ID / Wavelength: 0.97929 Å
DetectorType: MAR CCD 165 mm / Detector: CCD / Date: Jun 26, 2008
RadiationMonochromator: diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97929 Å / Relative weight: 1
ReflectionResolution: 1.69→44.77 Å / Num. obs: 83754 / % possible obs: 99.9 % / Observed criterion σ(I): 10 / Redundancy: 7 % / Biso Wilson estimate: 17.57 Å2 / Rsym value: 0.106 / Net I/σ(I): 7.4
Reflection shellResolution: 1.69→1.78 Å / Redundancy: 7 % / Mean I/σ(I) obs: 3.4 / Num. unique all: 16267 / Rsym value: 0.487 / % possible all: 99.9

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Processing

Software
NameVersionClassificationNB
REFMAC5.2.0019refinement
PDB_EXTRACT3.006data extraction
MOSFLMdata reduction
SCALAdata scaling
SHELXSphasing
RefinementResolution: 1.69→19.63 Å / Cor.coef. Fo:Fc: 0.964 / Cor.coef. Fo:Fc free: 0.949 / Occupancy max: 1 / Occupancy min: 0.2 / SU B: 1.932 / SU ML: 0.065 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.099 / ESU R Free: 0.099
Stereochemistry target values: MAXIMUM LIKELIHOOD WITH PHASES
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2504 3 %RANDOM
Rwork0.161 ---
obs0.162 82377 98.24 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso max: 54.38 Å2 / Biso mean: 16.993 Å2 / Biso min: 5.74 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refinement stepCycle: LAST / Resolution: 1.69→19.63 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5941 0 1 806 6748
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0226070
X-RAY DIFFRACTIONr_bond_other_d0.0010.023928
X-RAY DIFFRACTIONr_angle_refined_deg1.3061.968316
X-RAY DIFFRACTIONr_angle_other_deg0.93739618
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.7875834
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.6223.562233
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.35715891
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.5241545
X-RAY DIFFRACTIONr_chiral_restr0.0790.2987
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.026968
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021193
X-RAY DIFFRACTIONr_nbd_refined0.2080.21250
X-RAY DIFFRACTIONr_nbd_other0.1910.24244
X-RAY DIFFRACTIONr_nbtor_refined0.1640.23020
X-RAY DIFFRACTIONr_nbtor_other0.0840.23064
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1520.2546
X-RAY DIFFRACTIONr_metal_ion_refined0.0880.23
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2370.217
X-RAY DIFFRACTIONr_symmetry_vdw_other0.260.291
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1890.255
X-RAY DIFFRACTIONr_mcbond_it1.15224147
X-RAY DIFFRACTIONr_mcbond_other0.2921657
X-RAY DIFFRACTIONr_mcangle_it1.69136450
X-RAY DIFFRACTIONr_scbond_it2.11932139
X-RAY DIFFRACTIONr_scangle_it3.18651852
LS refinement shellResolution: 1.695→1.738 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 140 -
Rwork0.248 5426 -
all-5566 -
obs--91.25 %

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