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- PDB-2fvh: Crystal Structure of Rv1848, a Urease Gamma Subunit UreA (Urea am... -

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Basic information

Entry
Database: PDB / ID: 2fvh
TitleCrystal Structure of Rv1848, a Urease Gamma Subunit UreA (Urea amidohydrolase), from Mycobacterium Tuberculosis
ComponentsUrease gamma subunit
KeywordsHYDROLASE / Protein: UreA homolog / Structural Genomics / PSI / Protein Structure Initiative / TB Structural Genomics Consortium / TBSGC
Function / homology
Function and homology information


urease / urease activity / urea catabolic process / nickel cation binding / cytoplasm
Similarity search - Function
Urease; subunit A / Urease, gamma-like subunit / Urease, gamma subunit / Urease, gamma/gamma-beta subunit / Urease, gamma subunit superfamily / : / Urease, gamma subunit / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Urease subunit gamma / Urease subunit gamma
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.8 Å
AuthorsBursey, E.H. / Yu, M. / TB Structural Genomics Consortium (TBSGC) / Lekin, T. / Rupp, B. / Kim, C.Y. / Rho, B.S. / Terwilliger, T.C.
CitationJournal: To be Published
Title: Crystal Structure of Rv1848, a Urease Gamma Subunit UreA (Urea amidohydrolase), from Mycobacterium Tuberculosis
Authors: Bursey, E.H. / Yu, M. / Segelke, B.W. / Lekin, T. / Rupp, B. / Kim, C.Y. / Rho, B.S. / Terwilliger, T.C. / Hung, L.-W.
History
DepositionJan 30, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Feb 7, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Urease gamma subunit
B: Urease gamma subunit
C: Urease gamma subunit


Theoretical massNumber of molelcules
Total (without water)39,5763
Polymers39,5763
Non-polymers00
Water2,954164
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3700 Å2
ΔGint-3 kcal/mol
Surface area14860 Å2
MethodPISA
Unit cell
Length a, b, c (Å)109.988, 109.988, 40.873
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number168
Space group name H-MP6
DetailsThe biological assembly is likely to be a trimer as in the crystal assymmetric unit.

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Components

#1: Protein Urease gamma subunit / Urea amidohydrolase gamma subunit


Mass: 13191.990 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H32Rv / Gene: ureA / Plasmid: Custom / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21/DE3 / References: UniProt: P0A676, UniProt: P9WFE7*PLUS, urease
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 164 / 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: 1.8 Å3/Da / Density % sol: 31.76 %
Crystal growTemperature: 294 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 1.1% 2-Butanol, 23.76% Poly Ethylene Glycol 750MME, 0.16% Glycerol, 0.1M Sodium Cacodylate pH 5.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Nov 28, 2001
RadiationMonochromator: Si111 / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.75→50 Å / Num. all: 28667 / Num. obs: 27463 / % possible obs: 95.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Rmerge(I) obs: 0.043 / Net I/σ(I): 28
Reflection shellResolution: 1.75→1.81 Å / Mean I/σ(I) obs: 2.2 / % possible all: 79.4

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
DENZOdata reduction
SCALEPACKdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.8→27.02 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.938 / SU B: 5.635 / SU ML: 0.088 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.138 / ESU R Free: 0.134 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22946 1311 5.1 %RANDOM
Rwork0.18382 ---
obs0.18625 24482 97.3 %-
all-25793 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.717 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20.01 Å20 Å2
2--0.03 Å20 Å2
3----0.04 Å2
Refinement stepCycle: LAST / Resolution: 1.8→27.02 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2290 0 0 164 2454
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0212299
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.6021.9813112
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.1255294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.38122.075106
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.69715396
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.8021533
X-RAY DIFFRACTIONr_chiral_restr0.1010.2365
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021738
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2290.21196
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3080.21590
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2170
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.230.276
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1480.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.1921.51514
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.77822357
X-RAY DIFFRACTIONr_scbond_it3.2513840
X-RAY DIFFRACTIONr_scangle_it5.1574.5755
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.301 92 -
Rwork0.22 1648 -
obs--88.87 %
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)
11.19340.0630.26751.4187-0.02971.1359-0.01370.09640.03340.00290.03580.0433-0.14510.0867-0.0221-0.0734-0.0095-0.0066-0.06680.0097-0.057214.27425.3322.922
21.93311.05290.03061.8711-0.3813.082-0.0898-0.0155-0.1691-0.03130.0725-0.3252-0.26360.27520.0173-0.055-0.05820.0119-0.085-0.0245-0.011838.10838.52525.585
30.9980.2746-0.30613.187-1.43672.75420.0451-0.16640.11320.1379-0.0881-0.1722-0.02780.11990.043-0.07850.0174-0.0165-0.08120.0026-0.054131.02120.60545.067
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA2 - 10022 - 120
2X-RAY DIFFRACTION2BB2 - 10022 - 120
3X-RAY DIFFRACTION3CC2 - 10022 - 120

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