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- PDB-2we7: Crystal structure of Mycobacterium tuberculosis Rv0376c homologue... -

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Basic information

Entry
Database: PDB / ID: 2we7
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
Xanthine dehydrogenase
Similarity search - Component
Biological speciesMycolicibacterium smegmatis MC2 155 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.9 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 1.2Nov 6, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Source and taxonomy / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / entity / entity_src_nat / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / pdbx_struct_mod_residue / pdbx_struct_oper_list / struct_conn / struct_ref
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _entity.pdbx_ec / _entity_src_nat.pdbx_beg_seq_num / _entity_src_nat.pdbx_end_seq_num / _entity_src_nat.pdbx_organism_scientific / _pdbx_database_status.status_code_sf / _pdbx_struct_assembly_gen.oper_expression / _pdbx_struct_assembly_prop.value / _pdbx_struct_mod_residue.details / _pdbx_struct_oper_list.matrix[1][1] / _pdbx_struct_oper_list.matrix[1][2] / _pdbx_struct_oper_list.matrix[2][1] / _pdbx_struct_oper_list.matrix[2][2] / _pdbx_struct_oper_list.name / _pdbx_struct_oper_list.symmetry_operation / _pdbx_struct_oper_list.vector[3] / _struct_conn.pdbx_leaving_atom_flag / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Xanthine dehydrogenase
B: Xanthine dehydrogenase


Theoretical massNumber of molelcules
Total (without water)81,5622
Polymers81,5622
Non-polymers00
Water37821
1
A: Xanthine dehydrogenase

A: Xanthine dehydrogenase


Theoretical massNumber of molelcules
Total (without water)81,5622
Polymers81,5622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation11_554-x+y,y,-z-1/21
Buried area1990 Å2
ΔGint-13 kcal/mol
Surface area29910 Å2
MethodPISA
2
B: Xanthine dehydrogenase

B: Xanthine dehydrogenase


Theoretical massNumber of molelcules
Total (without water)81,5622
Polymers81,5622
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation7_555y,x,-z1
Buried area1650 Å2
ΔGint-12 kcal/mol
Surface area30080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)101.039, 101.039, 316.574
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Xanthine dehydrogenase


Mass: 40781.000 Da / Num. of mol.: 2 / Source method: isolated from a natural source
Source: (natural) Mycolicibacterium smegmatis MC2 155 (bacteria)
Strain: MC2 155 / References: UniProt: A0QQG1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 21 / 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: 2.66 Å3/Da / Density % sol: 53.8 % / 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: 0.9795
DetectorType: ADSC CCD / Detector: CCD / Date: Jul 11, 2007 / Details: MIRRORS
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.9→50 Å / Num. obs: 21926 / % possible obs: 99.9 % / Redundancy: 26.2 % / Rmerge(I) obs: 0.12 / Net I/σ(I): 63.91
Reflection shellResolution: 2.9→50 Å / Redundancy: 23.2 % / Rmerge(I) obs: 0.35 / Mean I/σ(I) obs: 12.1 / % possible all: 99.9

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Processing

Software
NameVersionClassification
DENZOdata reduction
HKL-2000data scaling
SOLVEphasing
RESOLVEphasing
REFMAC5.2.0019refinement
RefinementMethod to determine structure: SAD
Starting model: NONE

Resolution: 2.9→38.29 Å / Cor.coef. Fo:Fc: 0.935 / Cor.coef. Fo:Fc free: 0.893 / SU B: 27.764 / SU ML: 0.25 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 1.885 / ESU R Free: 0.368 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1135 5.2 %RANDOM
Rwork0.195 ---
obs0.198 20666 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 49.91 Å2
Baniso -1Baniso -2Baniso -3
1-0.29 Å20.14 Å20 Å2
2--0.29 Å20 Å2
3----0.43 Å2
Refinement stepCycle: LAST / Resolution: 2.9→38.29 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5006 0 0 21 5027
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0225120
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2881.9646983
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8045680
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.9722.227211
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.19615762
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.6411557
X-RAY DIFFRACTIONr_chiral_restr0.0870.2819
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023928
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2160.22237
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3110.23520
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1370.2192
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1890.256
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.5420.23
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.70333424
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.71655386
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it4.79981870
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it7.353111594
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: 2.9→2.98 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.3 89 -
Rwork0.243 1408 -
obs--100 %
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)
12.9933-0.77450.84814.81452.00231.8983-0.19020.07590.1129-0.09850.07610.2718-0.2803-0.08180.11410.04530.0179-0.00720.01270.02540.1914-23.382-21.026-57.299
22.9196-0.1738-1.22510.474-0.05220.7004-0.0785-0.1299-0.0540.08790.0644-0.080.01470.05760.0140.06910.0101-0.00260.0641-0.01820.17590.289-28.985-58.22
34.9679-1.76361.66320.8973-0.36373.3868-0.05130.21410.0272-0.0183-0.0762-0.08940.1065-0.19190.12750.1294-0.0151-0.02850.051-0.00740.324112.423-39.217-71.675
46.09260.06630.84522.96810.09195.01620.3143-0.766-0.37311.36350.3019-0.92240.54310.4961-0.61620.46510.1042-0.49910.3064-0.04110.431711.617-29.758-20.331
53.8335-1.4814-2.8360.98161.25185.60550.0707-0.4661-0.1880.18760.3181-0.01110.54270.3104-0.38880.2640.0802-0.12420.14650.0721-0.0773-7.124-29.771-24.184
63.62411.3815-0.88687.366-3.24477.64510.0170.323-0.0819-0.270.77781.20830.5795-0.8815-0.7948-0.10580.0275-0.06290.50370.20160.1394-30.004-22.636-10.612
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A4 - 116
2X-RAY DIFFRACTION2A117 - 292
3X-RAY DIFFRACTION3A293 - 359
4X-RAY DIFFRACTION4B4 - 104
5X-RAY DIFFRACTION5B105 - 238
6X-RAY DIFFRACTION6B239 - 359

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