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- PDB-2we8: Crystal structure of Mycobacterium tuberculosis Rv0376c homologue... -

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Basic information

Entry
Database: PDB / ID: 2we8
TitleCrystal structure of Mycobacterium tuberculosis Rv0376c homologue from Mycobacterium smegmatis
ComponentsXANTHINE DEHYDROGENASE
KeywordsOXIDOREDUCTASE
Function / homology
Function and homology information


XdhC- CoxI / XdhC Rossmann domain / : / XdhC and CoxI family / XdhC Rossmann domain / NAD(P)-binding Rossmann-like Domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACETATE ION / Xanthine dehydrogenase
Similarity search - Component
Biological speciesMYCOBACTERIUM SMEGMATIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCho, H.J. / Kang, B.S.
CitationJournal: To be Published
Title: Crystal Structure of Mycobacterium Tuberculosis Rv0376C Homologue from Mycobacterium Smegmatis
Authors: Cho, H.J. / Kang, B.S.
History
DepositionMar 29, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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 / _pdbx_database_status.status_code_sf / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: XANTHINE DEHYDROGENASE
B: XANTHINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)81,91512
Polymers81,0932
Non-polymers82210
Water3,585199
1
A: XANTHINE DEHYDROGENASE
hetero molecules

A: XANTHINE DEHYDROGENASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)82,73722
Polymers81,0932
Non-polymers1,64420
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation12_555x,x-y,-z+1/21
Buried area6340 Å2
ΔGint-21.7 kcal/mol
Surface area29520 Å2
MethodPISA
2
B: XANTHINE DEHYDROGENASE

B: XANTHINE DEHYDROGENASE


Theoretical massNumber of molelcules
Total (without water)81,0932
Polymers81,0932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_556x-y,-y,-z+11
Buried area1620 Å2
ΔGint-14.6 kcal/mol
Surface area29220 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.208, 101.208, 316.669
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11A-2147-

HOH

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Components

#1: Protein XANTHINE DEHYDROGENASE


Mass: 40546.531 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Details: RESIDUES 4-360 / Source: (natural) MYCOBACTERIUM SMEGMATIS (bacteria) / Strain: MC2 155 / References: UniProt: A0QQG1, xanthine dehydrogenase
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 7 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 199 / 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: 2.67 Å3/Da / Density % sol: 54 % / Description: NONE
Crystal growpH: 7.5
Details: 0.1 M CITRATE PH 4.8, 17% PEG 8000, 0.2 M AMMONIUM ACETATE AND 4% ETHANOL BY MICRO-SEEDING.

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Data collection

DiffractionMean temperature: 294 K
Diffraction sourceSource: SYNCHROTRON / Site: PAL/PLS / Beamline: 4A / Wavelength: 1
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 11, 2007 / Details: MIRRORS
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.16→50 Å / Num. obs: 51359 / % possible obs: 97.9 % / Redundancy: 18.7 % / Rmerge(I) obs: 0.11 / Net I/σ(I): 25.6
Reflection shellResolution: 2.16→2.24 Å / Redundancy: 3.4 % / Rmerge(I) obs: 0.1 / Mean I/σ(I) obs: 2.05 / % possible all: 83.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
DENZOdata reduction
HKL-2000data scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2WE7

2we7


Resolution: 2.3→33.73 Å / Cor.coef. Fo:Fc: 0.949 / Cor.coef. Fo:Fc free: 0.918 / SU B: 12.913 / SU ML: 0.158 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.238 / ESU R Free: 0.211 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORD CONTAINS RESIDUAL B FACTORS ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.251 2223 5.1 %RANDOM
Rwork0.199 ---
obs0.201 41413 99.8 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 54.81 Å2
Baniso -1Baniso -2Baniso -3
1--0.06 Å2-0.03 Å20 Å2
2---0.06 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 2.3→33.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5017 0 54 199 5270
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0110.0225176
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2891.9687049
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.855683
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.38722.201209
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.43515760
X-RAY DIFFRACTIONr_dihedral_angle_4_deg21.581556
X-RAY DIFFRACTIONr_chiral_restr0.0860.2824
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023945
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2050.22213
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.23497
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1650.2235
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.258
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.180.28
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.70933442
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.90655413
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.82881915
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.056111632
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: 2.3→2.36 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.333 169 -
Rwork0.259 2934 -
obs--99.04 %
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)
10.3042-0.1978-0.06251.57380.42570.3480.0083-0.00840.00060.05-0.0459-0.00640.01660.0020.0376-0.06-0.0191-0.0119-0.06070.0126-0.0394-26.9905-11.185297.5044
20.5886-0.3231-0.38481.92990.96432.35360.0524-0.08730.01290.09030.11020.0875-0.1144-0.2463-0.1626-0.004-0.03790.00890.01680.084-0.2789-29.1355-3.4363140.257
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 360
2X-RAY DIFFRACTION2B5 - 359

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