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- PDB-2chc: Structure of Rv3472(D26N), a function unknown protein from Mycoba... -

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Basic information

Entry
Database: PDB / ID: 2chc
TitleStructure of Rv3472(D26N), a function unknown protein from Mycobacterium tuberculosis
ComponentsPROTEIN RV3472
KeywordsHYPOTHETICAL PROTEIN / RV3472 / MYCOBACTERIUM / TUBERCULOSIS
Function / homologySnoaL-like domain / SnoaL-like domain / Nuclear Transport Factor 2; Chain: A, - #50 / NTF2-like domain superfamily / Nuclear Transport Factor 2; Chain: A, / Roll / Alpha Beta / SnoaL-like domain-containing protein
Function and homology information
Biological speciesMYCOBACTERIUM TUBERCULOSIS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.69 Å
AuthorsMa, Q. / Wilmanns, M.
CitationJournal: To be Published
Title: Structure of Rv3472(D26N), a Function Unknown Protein from Mycobacterium Tuberculosis
Authors: Ma, Q. / Wilmanns, M.
History
DepositionMar 13, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 1, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Jun 28, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.3Mar 7, 2018Group: Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name ..._entity_src_gen.pdbx_host_org_ncbi_taxonomy_id / _entity_src_gen.pdbx_host_org_scientific_name / _entity_src_gen.pdbx_host_org_strain / _entity_src_gen.pdbx_host_org_variant
Revision 1.4May 8, 2019Group: Data collection / Experimental preparation / Category: exptl_crystal_grow / Item: _exptl_crystal_grow.temp
Revision 1.5Jul 24, 2019Group: Data collection / Category: diffrn_source / Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.6May 8, 2024Group: Data collection / Database references / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: PROTEIN RV3472
B: PROTEIN RV3472
C: PROTEIN RV3472


Theoretical massNumber of molelcules
Total (without water)55,8543
Polymers55,8543
Non-polymers00
Water5,891327
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)60.339, 91.917, 191.987
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein PROTEIN RV3472


Mass: 18617.898 Da / Num. of mol.: 3 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) MYCOBACTERIUM TUBERCULOSIS (bacteria) / Strain: H37RV / Plasmid: PETM11 / Production host: Escherichia coli BL21(DE3) (bacteria) / Variant (production host): Rosetta pLySS / References: UniProt: O06337
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 327 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASP 26 TO ASN ENGINEERED RESIDUE IN CHAIN B, ASP 26 TO ASN ...ENGINEERED RESIDUE IN CHAIN A, ASP 26 TO ASN ENGINEERED RESIDUE IN CHAIN B, ASP 26 TO ASN ENGINEERED RESIDUE IN CHAIN C, ASP 26 TO ASN
Sequence detailsSOME RESIDUES ARE ALTERED DUE TO GENE CONSTRUCTION METHOD. ATOMS WITH VERY POOR ELECTRON DENSITY ...SOME RESIDUES ARE ALTERED DUE TO GENE CONSTRUCTION METHOD. ATOMS WITH VERY POOR ELECTRON DENSITY ARE NOT BUILT INTO THE MODEL.

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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: 2.4 Å3/Da / Density % sol: 48 %
Crystal growTemperature: 293 K / pH: 7.4
Details: 0.1M HEPES PH7.4, 0.2M MGCL2, 25% PEG400, 20 DEGREES C, pH 7.40

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: BW7B / Wavelength: 0.8424
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 1, 2005 / Details: MIRROR
RadiationMonochromator: TRIANGULAR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8424 Å / Relative weight: 1
ReflectionResolution: 1.69→37.3 Å / Num. obs: 60209 / % possible obs: 99.6 % / Redundancy: 6.5 % / Biso Wilson estimate: 23.6 Å2 / Rmerge(I) obs: 0.04 / Net I/σ(I): 24.67
Reflection shellResolution: 1.69→1.79 Å / Redundancy: 5.71 % / Rmerge(I) obs: 0.32 / Mean I/σ(I) obs: 5.23 / % possible all: 98.6

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Processing

Software
NameVersionClassification
ARP/wARPmodel building
SCALEPACKdata scaling
SHELXDphasing
SHELXEphasing
DMphasing
ARP/wARPphasing
REFMAC5.2.0005refinement
RefinementMethod to determine structure: SAD / Resolution: 1.69→37.32 Å / Cor.coef. Fo:Fc: 0.966 / Cor.coef. Fo:Fc free: 0.954 / SU B: 3.356 / SU ML: 0.056 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.088 / ESU R Free: 0.091 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.199 2971 4.9 %THIN SHELLS
Rwork0.164 ---
obs0.166 57236 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 22.68 Å2
Baniso -1Baniso -2Baniso -3
1-0.04 Å20 Å20 Å2
2---0.13 Å20 Å2
3---0.09 Å2
Refinement stepCycle: LAST / Resolution: 1.69→37.32 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3668 0 0 327 3995
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0190.0213745
X-RAY DIFFRACTIONr_bond_other_d0.0010.023480
X-RAY DIFFRACTIONr_angle_refined_deg1.7551.9365085
X-RAY DIFFRACTIONr_angle_other_deg0.89537909
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.2875486
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.50121.716169
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.02915566
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.4341546
X-RAY DIFFRACTIONr_chiral_restr0.1150.2572
X-RAY DIFFRACTIONr_gen_planes_refined0.010.024320
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02858
X-RAY DIFFRACTIONr_nbd_refined0.2260.2729
X-RAY DIFFRACTIONr_nbd_other0.1930.23636
X-RAY DIFFRACTIONr_nbtor_refined0.1840.21861
X-RAY DIFFRACTIONr_nbtor_other0.0850.22598
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.2192
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2470.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.30.297
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2040.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.3441.52430
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.14623777
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it3.11231498
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.8954.51308
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: 1.69→1.73 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.293 110
Rwork0.217 4185
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)
10.91140.19950.16761.59020.38341.20940.0356-0.06380.09760.1096-0.06930.0438-0.0535-0.06870.0337-0.05520.0053-0.0017-0.05190.0062-0.0324.688632.854979.2823
21.71120.00670.47562.64880.53830.48880.00140.21980.122-0.5251-0.11830.1096-0.02070.10160.11690.07930.0675-0.00260.0090.0682-0.04420.282737.805362.2178
31.1986-0.32050.30291.2504-0.01491.33890.05710.10860.0210.0426-0.0128-0.20090.02420.1511-0.0444-0.04940.0155-0.0012-0.0320.0046-0.0438.75415.672970.3106
41.48130.1453-0.28680.1248-0.44141.6606-0.02740.3723-0.2663-0.04870.0226-0.01470.31540.01120.00480.02850.02650.01910.0644-0.0595-0.060332.29449.860355.4221
51.34760.50170.00941.67580.16540.70530.11-0.1011-0.13960.1731-0.0716-0.01010.1589-0.0756-0.0384-0.0252-0.0365-0.0039-0.05490.0137-0.049817.97519.527681.7803
61.37181.746-0.23572.239-0.20520.5785-0.17760.1590.1488-0.11020.13510.37680.106-0.14130.0425-0.0408-0.0406-0.05030.04130.03250.10955.458111.207469.6019
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A-1 - 129
2X-RAY DIFFRACTION2A130 - 167
3X-RAY DIFFRACTION3B6 - 129
4X-RAY DIFFRACTION4B130 - 166
5X-RAY DIFFRACTION5C7 - 129
6X-RAY DIFFRACTION6C130 - 165

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