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- PDB-2wam: Crystal structure of Mycobacterium tuberculosis unknown function ... -

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Basic information

Entry
Database: PDB / ID: 2wam
TitleCrystal structure of Mycobacterium tuberculosis unknown function protein Rv2714
ComponentsCONSERVED HYPOTHETICAL ALANINE AND LEUCINE RICH PROTEIN
KeywordsUNKNOWN FUNCTION
Function / homology
Function and homology information


protein homotrimerization / plasma membrane
Similarity search - Function
Rv2714-like / PAC-like subunit / Helix Hairpins - #100 / Proteasome assembly chaperone 2 / Proteasome assembly chaperone 2 superfamily / PAC2 family / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich ...Rv2714-like / PAC-like subunit / Helix Hairpins - #100 / Proteasome assembly chaperone 2 / Proteasome assembly chaperone 2 superfamily / PAC2 family / Helix Hairpins / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.6 Å
AuthorsBellinzoni, M. / Grana, M. / Buschiazzo, A. / Miras, I. / Haouz, A. / Alzari, P.M.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2009
Title: Structure of Mycobacterium Tuberculosis Rv2714, a Representative of a Duplicated Gene Family in Actinobacteria.
Authors: Grana, M. / Bellinzoni, M. / Miras, I. / Fiex-Vandal, C. / Haouz, A. / Shepard, W. / Buschiazzo, A. / Alzari, P.M.
History
DepositionFeb 9, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 6, 2009Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 1, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: CONSERVED HYPOTHETICAL ALANINE AND LEUCINE RICH PROTEIN
B: CONSERVED HYPOTHETICAL ALANINE AND LEUCINE RICH PROTEIN
C: CONSERVED HYPOTHETICAL ALANINE AND LEUCINE RICH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)116,6365
Polymers116,4523
Non-polymers1842
Water4,197233
1
A: CONSERVED HYPOTHETICAL ALANINE AND LEUCINE RICH PROTEIN
B: CONSERVED HYPOTHETICAL ALANINE AND LEUCINE RICH PROTEIN
C: CONSERVED HYPOTHETICAL ALANINE AND LEUCINE RICH PROTEIN
hetero molecules

A: CONSERVED HYPOTHETICAL ALANINE AND LEUCINE RICH PROTEIN
B: CONSERVED HYPOTHETICAL ALANINE AND LEUCINE RICH PROTEIN
C: CONSERVED HYPOTHETICAL ALANINE AND LEUCINE RICH PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)233,27210
Polymers232,9036
Non-polymers3684
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area22250 Å2
ΔGint-90.37 kcal/mol
Surface area71270 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area8060 Å2
ΔGint-28.28 kcal/mol
Surface area38700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)140.493, 140.493, 129.770
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(0.53, -0.846, 0.061), (-0.358, -0.159, 0.92), (-0.768, -0.51, -0.387)-50.86725, -61.48272, -43.94377
2given(0.51255, -0.28587, -0.80968), (-0.85845, -0.1498, -0.49053), (0.01894, 0.94649, -0.32219)-25.30401, -74.92794, 43.5372

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Components

#1: Protein CONSERVED HYPOTHETICAL ALANINE AND LEUCINE RICH PROTEIN / RV2714


Mass: 38817.207 Da / Num. of mol.: 3 / Fragment: RESIDUES 2-323
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PDEST17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)PLYSS / References: UniProt: O07213
#2: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 233 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsN-TERMINAL SEQUENCE MSYYHHHHHHLESTSLYKKAGSENLYFQG IS A CLONING ARTIFACT (PURIFICATION TAG)

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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: 3.18 Å3/Da / Density % sol: 61.3 % / Description: NONE
Crystal growpH: 6.5 / Details: pH 6.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Wavelength: 0.931
DetectorType: ADSC CCD / Detector: CCD / Date: Jun 20, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 2.6→47.66 Å / Num. obs: 45795 / % possible obs: 99.8 % / Observed criterion σ(I): 2 / Redundancy: 3.7 % / Biso Wilson estimate: 55.8 Å2 / Rmerge(I) obs: 0.07 / Net I/σ(I): 14.8
Reflection shellResolution: 2.6→2.74 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.53 / Mean I/σ(I) obs: 2.4 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: UNPUBLISHED

Resolution: 2.6→44.38 Å / SU ML: 0.33 / σ(F): 1.35 / Phase error: 20.31 / Stereochemistry target values: ML
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. ATOM RECORDS CONTAIN ISOTROPIC EQUIVALENTS OF THE SUM OF TLS AND RESIDUAL B FACTORS. ANISOU RECORDS CONTAIN SUM OF TLS AND RESIDUAL U FACTORS.
RfactorNum. reflection% reflection
Rfree0.221 2310 5.1 %
Rwork0.175 --
obs0.177 45756 99.8 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 45.03 Å2 / ksol: 0.34 e/Å3
Displacement parametersBiso mean: 50.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.5799 Å2-0 Å2-0 Å2
2--0.5799 Å20 Å2
3----1.1599 Å2
Refinement stepCycle: LAST / Resolution: 2.6→44.38 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6580 0 12 233 6825
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0076733
X-RAY DIFFRACTIONf_angle_d1.0139169
X-RAY DIFFRACTIONf_dihedral_angle_d16.4582419
X-RAY DIFFRACTIONf_chiral_restr0.0671048
X-RAY DIFFRACTIONf_plane_restr0.0051215
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.6-2.65310.30031420.23662534X-RAY DIFFRACTION100
2.6531-2.71080.32291430.24182493X-RAY DIFFRACTION100
2.7108-2.77380.30281380.23382531X-RAY DIFFRACTION100
2.7738-2.84320.28631460.22612509X-RAY DIFFRACTION100
2.8432-2.920.27541560.21512527X-RAY DIFFRACTION100
2.92-3.0060.29681310.20532531X-RAY DIFFRACTION100
3.006-3.1030.25031370.20532530X-RAY DIFFRACTION100
3.103-3.21380.24151420.18552542X-RAY DIFFRACTION100
3.2138-3.34250.21231210.1752559X-RAY DIFFRACTION100
3.3425-3.49450.241350.16422547X-RAY DIFFRACTION100
3.4945-3.67870.18871330.14392569X-RAY DIFFRACTION100
3.6787-3.9090.17051120.12942568X-RAY DIFFRACTION100
3.909-4.21060.16621260.1272564X-RAY DIFFRACTION100
4.2106-4.6340.16331460.11792569X-RAY DIFFRACTION100
4.634-5.30360.16061410.12882588X-RAY DIFFRACTION100
5.3036-6.67830.19551380.16272602X-RAY DIFFRACTION100
6.6783-44.38610.19591230.17012683X-RAY DIFFRACTION98
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)
10.4962-0.18720.40480.38290.09661.5154-0.07110.07740.0956-0.05620.0357-0.0707-0.15640.200500.1496-0.0268-0.00090.21070.01410.26596.5886-48.16089.0899
20.82830.0919-0.42850.9965-0.21980.93190.0350.2007-0.0244-0.249-0.0358-0.15240.0006-0.016300.19270.03440.09020.20750.01510.1112-6.1424-47.5262-27.4581
30.3779-0.02610.31191.12080.55950.4980.04850.0299-0.07830.116-0.03720.09090.01160.0097-00.24510.00490.03810.228-0.01470.217-16.653-77.3881-5.2737
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1CHAIN A
2X-RAY DIFFRACTION2CHAIN B
3X-RAY DIFFRACTION3CHAIN C

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