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- PDB-1tq8: Crystal Structure of protein Rv1636 from Mycobacterium tuberculos... -

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Basic information

Entry
Database: PDB / ID: 1tq8
TitleCrystal Structure of protein Rv1636 from Mycobacterium tuberculosis H37Rv
Componentshypothetical protein Rv1636
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / HypotheticalProtein / RV1636 / MTCY01B2.28 / MT1672 / STRUCTURAL GENOMICS TARGET / T1533 / NYSGXRC / PSI / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


cell wall / response to antibiotic / plasma membrane
Similarity search - Function
Universal stress protein A family / UspA / Universal stress protein family / HUPs / Rossmann-like alpha/beta/alpha sandwich fold / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Universal stress protein MT1672 / Universal stress protein Rv1636
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.4 Å
AuthorsRajashankar, K.R. / Kniewel, R. / Solorzano, V. / Lima, C.D. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of hypothetical protein Rv1636 from Mycobacterium tuberculosis H37Rv
Authors: RAJASHANKAR, K.R. / KNIEWEL, R. / SOLORZANO, V. / LIMA, C.D.
History
DepositionJun 16, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jun 29, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / struct_conn / struct_ref_seq_dif
Item: _audit_author.identifier_ORCID / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Apr 3, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / refine
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _refine.pdbx_starting_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein Rv1636
B: hypothetical protein Rv1636
C: hypothetical protein Rv1636
D: hypothetical protein Rv1636
E: hypothetical protein Rv1636
F: hypothetical protein Rv1636


Theoretical massNumber of molelcules
Total (without water)103,3566
Polymers103,3566
Non-polymers00
Water3,891216
1
A: hypothetical protein Rv1636
B: hypothetical protein Rv1636
C: hypothetical protein Rv1636
D: hypothetical protein Rv1636


Theoretical massNumber of molelcules
Total (without water)68,9044
Polymers68,9044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14010 Å2
ΔGint-119 kcal/mol
Surface area21460 Å2
MethodPISA
2
E: hypothetical protein Rv1636
F: hypothetical protein Rv1636

E: hypothetical protein Rv1636
F: hypothetical protein Rv1636


Theoretical massNumber of molelcules
Total (without water)68,9044
Polymers68,9044
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_545-x,-y-1,z1
Unit cell
Length a, b, c (Å)72.829, 121.042, 119.751
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein
hypothetical protein Rv1636


Mass: 17226.043 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Strain: H37Rv / Gene: Rv1636 / Plasmid: PET T7 / Production host: Escherichia coli (E. coli) / Strain (production host): B834, DE3 / References: UniProt: O06153, UniProt: P9WFC9*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / 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: 2.57 Å3/Da / Density % sol: 51.79 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 1.6M NaCl, 0.1M NaAcetate, pH 5.0, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONNSLS X9A10.98
SYNCHROTRONNSLS X29A20.98
Detector
TypeIDDetectorDate
MARRESEARCH1CCDApr 30, 2004
ADSC QUANTUM 3142CCDJun 5, 2004
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED Si(111)SINGLE WAVELENGTHMx-ray1
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 2.4→30 Å / Num. all: 79424 / Num. obs: 79424 / % possible obs: 99.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.74 % / Biso Wilson estimate: 41.9 Å2 / Rsym value: 0.064 / Net I/σ(I): 19.54
Reflection shellResolution: 2.4→2.49 Å / Redundancy: 2.39 % / Num. unique all: 7444 / Rsym value: 0.423 / % possible all: 93.4

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Processing

Software
NameVersionClassification
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 2.4→29.94 Å / Rfactor Rfree error: 0.004 / Data cutoff high absF: 509799.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: Residues 56 to 76 of molecules A, B, C, D and F and residues 56 to 77 of molecule E seem to be disordered as they were not located in the experimental electron density map.
RfactorNum. reflection% reflectionSelection details
Rfree0.262 3706 4.9 %RANDOM
Rwork0.221 ---
obs0.221 75562 94.4 %-
all-75562 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.1307 Å2 / ksol: 0.30719 e/Å3
Displacement parametersBiso mean: 51.1 Å2
Baniso -1Baniso -2Baniso -3
1-7.49 Å20 Å20 Å2
2---0.67 Å20 Å2
3----6.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.4 Å0.32 Å
Luzzati d res low-5 Å
Luzzati sigma a0.41 Å0.34 Å
Refinement stepCycle: LAST / Resolution: 2.4→29.94 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5537 0 0 216 5753
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.1
X-RAY DIFFRACTIONc_dihedral_angle_d22.8
X-RAY DIFFRACTIONc_improper_angle_d0.86
X-RAY DIFFRACTIONc_mcbond_it1.551.5
X-RAY DIFFRACTIONc_mcangle_it2.672
X-RAY DIFFRACTIONc_scbond_it2.212
X-RAY DIFFRACTIONc_scangle_it3.392.5
LS refinement shellResolution: 2.4→2.55 Å / Rfactor Rfree error: 0.015 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.363 582 5.3 %
Rwork0.33 10462 -
obs--83.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP

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