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- PDB-1xkf: Crystal structure of Hypoxic Response Protein I (HRPI) with two c... -

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Basic information

Entry
Database: PDB / ID: 1xkf
TitleCrystal structure of Hypoxic Response Protein I (HRPI) with two coordinated zinc ions
Componentshypothetical protein RV2626CHypothesis
KeywordsUNKNOWN FUNCTION / CBS domain
Function / homology
Function and homology information


symbiont-mediated perturbation of host immune response / response to host immune response / peptidoglycan-based cell wall / response to hypoxia / extracellular region / metal ion binding / plasma membrane / cytosol
Similarity search - Function
CBS-domain / CBS-domain / CBS domain superfamily / Domain in cystathionine beta-synthase and other proteins. / CBS domain / CBS domain / CBS domain profile. / Roll / Alpha Beta
Similarity search - Domain/homology
Hypoxic response protein 1 / Hypoxic response protein 1
Similarity search - Component
Biological speciesMycobacterium tuberculosis (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.9 Å
AuthorsSharpe, M.L. / Baker, E.N. / Lott, J.S.
CitationJournal: J.Mol.Biol. / Year: 2008
Title: The structure and unusual protein chemistry of hypoxic response protein 1, a latency antigen and highly expressed member of the DosR regulon in Mycobacterium tuberculosis
Authors: Sharpe, M.L. / Gao, C. / Kendall, S.L. / Baker, E.N. / Lott, J.S.
History
DepositionSep 28, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Oct 11, 2005Provider: repository / Type: Initial release
Revision 1.1Jan 8, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein RV2626C
B: hypothetical protein RV2626C
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,1404
Polymers29,0092
Non-polymers1312
Water3,675204
1
A: hypothetical protein RV2626C
hetero molecules

B: hypothetical protein RV2626C


Theoretical massNumber of molelcules
Total (without water)29,1404
Polymers29,0092
Non-polymers1312
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_455x-1,y,z1
Buried area1420 Å2
ΔGint-11 kcal/mol
Surface area12160 Å2
MethodPISA
2


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1450 Å2
ΔGint-54 kcal/mol
Surface area12340 Å2
MethodPISA
Unit cell
Length a, b, c (Å)40.650, 50.940, 129.190
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein hypothetical protein RV2626C / Hypothesis / HYPOXIC RESPONSE PROTEIN I


Mass: 14504.354 Da / Num. of mol.: 2 / Fragment: residues 1-127
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycobacterium tuberculosis (bacteria) / Gene: Rv2626c / Plasmid: pET151 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O06186, UniProt: P9WJA3*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 204 / 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: 2.3 Å3/Da / Density % sol: 46.3 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 6.1
Details: methoxyPEG 5000, MES/KOH, pH 6.1, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 113 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RUH3R / Wavelength: 1.5418
DetectorType: MAR scanner 345 mm plate / Detector: IMAGE PLATE / Date: Dec 5, 2003 / Details: MSC Osmic optics
RadiationMonochromator: Ni FILTER / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→30 Å / Num. all: 21923 / Num. obs: 21474 / % possible obs: 97.7 % / Redundancy: 9.5 % / Biso Wilson estimate: 18.7 Å2 / Limit h max: 20 / Limit h min: 0 / Limit k max: 26 / Limit k min: 0 / Limit l max: 67 / Limit l min: 0 / Observed criterion F max: 114576.01 / Observed criterion F min: 1.1 / Rsym value: 0.125 / Net I/σ(I): 56.6
Reflection shellResolution: 1.9→1.97 Å / Mean I/σ(I) obs: 2.16 / Num. unique all: 2045 / Rsym value: 0.813 / % possible all: 94.5

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
DENZOdata reduction
SCALEPACKdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.9→20.47 Å / Rfactor Rfree error: 0.007 / Occupancy max: 1 / Occupancy min: 1 / Cross valid method: THROUGHOUT
RfactorNum. reflection% reflectionSelection details
Rfree0.235 1071 5 %random
Rwork0.206 ---
all-21901 --
obs-21428 97.8 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 47.4954 Å2 / ksol: 0.370983 e/Å3
Displacement parametersBiso max: 51.84 Å2 / Biso mean: 22.37 Å2 / Biso min: 11.02 Å2
Baniso -1Baniso -2Baniso -3
1--1.62 Å20 Å20 Å2
2--3.05 Å20 Å2
3----1.43 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
nonpolymerX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.17 Å0.16 Å
Luzzati d res high-1.9
Refinement stepCycle: LAST / Resolution: 1.9→20.47 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1813 0 2 204 2019
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.005
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_torsion_deg22.9
X-RAY DIFFRACTIONx_torsion_impr_deg0.75
X-RAY DIFFRACTIONx_mcbond_it1.311.5
X-RAY DIFFRACTIONx_mcangle_it1.952
X-RAY DIFFRACTIONx_scbond_it2.32
X-RAY DIFFRACTIONx_scangle_it3.382.5
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 8

Resolution (Å)Rfactor RfreeNum. reflection Rfree% reflection Rfree (%)Rfactor RworkNum. reflection RworkRfactor Rfree errorNum. reflection allNum. reflection obs% reflection obs (%)
1.9-1.990.3651003.90.31324640.0372706256494.8
1.99-2.090.2581375.30.23224480.0222681258596.4
2.09-2.220.2191274.90.19624840.0192692261197
2.22-2.390.2581254.80.20125060.0232715263196.9
2.39-2.630.2481405.20.20325370.0212708267798.9
2.63-3.010.2361505.60.20825470.0192732269798.7
3.01-3.790.2371485.40.19326100.022774275899.4
3.79-20.470.20414450.19827610.0172907290599.9
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top
X-RAY DIFFRACTION4ion.paramion.top

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