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- PDB-1y5h: Crystal structure of truncated Se-Met Hypoxic Response Protein I ... -

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Basic information

Entry
Database: PDB / ID: 1y5h
TitleCrystal structure of truncated Se-Met Hypoxic Response Protein I (HRPI)
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 / SYNCHROTRON / MAD / Resolution: 1.5 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
DepositionDec 2, 2004Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 15, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 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


Theoretical massNumber of molelcules
Total (without water)29,5732
Polymers29,5732
Non-polymers00
Water2,450136
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1420 Å2
ΔGint-11 kcal/mol
Surface area11580 Å2
MethodPISA
Unit cell
Length a, b, c (Å)77.452, 41.064, 78.395
Angle α, β, γ (deg.)90.00, 108.41, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein hypothetical protein RV2626C / Hypothesis / hypoxic response protein I


Mass: 14786.712 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 / Production host: Escherichia coli (E. coli) / Strain (production host): DL41 / References: UniProt: O06186, UniProt: P9WJA3*PLUS
#2: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 136 / 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 Å3/Da / Density % sol: 39.3 % / Description: the file contains Friedel pairs
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 9
Details: ammonium sulphate, boric acid/KOH, pH 9.0, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.9793, 0.9796, 0.9537
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jul 3, 2004 / Details: Toroidal mirror
RadiationMonochromator: Double-crystal, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.97931
20.97961
30.95371
ReflectionResolution: 1.5→50 Å / Num. all: 73443 / Num. obs: 66279 / % possible obs: 92.4 % / Redundancy: 6.2 % / Biso Wilson estimate: 22.5 Å2 / Limit h max: 51 / Limit h min: 0 / Limit k max: 27 / Limit k min: 0 / Limit l max: 49 / Limit l min: -52 / Observed criterion F max: 118610.22 / Observed criterion F min: 0.6 / Rsym value: 0.113 / Net I/σ(I): 20.97
Reflection shellResolution: 1.5→1.55 Å / Redundancy: 3.2 % / Mean I/σ(I) obs: 1.77 / Num. unique all: 2395 / Rsym value: 0.464 / % possible all: 63.7

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Processing

Software
NameVersionClassificationNB
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SHELXDphasing
SHELXEmodel building
RefinementMethod to determine structure: MAD / Resolution: 1.5→38.06 Å / Rfactor Rfree error: 0.003 / Occupancy max: 1 / Occupancy min: 1 / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / Stereochemistry target values: Engh & Huber / Details: the file contains Friedel pairs
RfactorNum. reflection% reflectionSelection details
Rfree0.233 6466 9.8 %random
Rwork0.222 ---
all-73456 --
obs-66279 90.2 %-
Solvent computationSolvent model: CNS bulk solvent model used / Bsol: 53.4993 Å2 / ksol: 0.385557 e/Å3
Displacement parametersBiso max: 56.94 Å2 / Biso mean: 26.8 Å2 / Biso min: 13.63 Å2
Baniso -1Baniso -2Baniso -3
1-4.93 Å20 Å22.89 Å2
2---0.41 Å20 Å2
3----4.52 Å2
Refine Biso
ClassRefine-IDTreatment
polymerX-RAY DIFFRACTIONisotropic
waterX-RAY DIFFRACTIONisotropic
Refine analyze
FreeObs
Luzzati coordinate error0.21 Å0.19 Å
Luzzati d res low-5 Å
Luzzati sigma a0.21 Å0.23 Å
Luzzati d res high-1.5
Refinement stepCycle: LAST / Resolution: 1.5→38.06 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1760 0 0 136 1896
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONx_bond_d0.004
X-RAY DIFFRACTIONx_angle_deg1.2
X-RAY DIFFRACTIONx_torsion_deg23.4
X-RAY DIFFRACTIONx_torsion_impr_deg0.76
X-RAY DIFFRACTIONx_mcbond_it1.341.5
X-RAY DIFFRACTIONx_mcangle_it2.122
X-RAY DIFFRACTIONx_scbond_it2.152
X-RAY DIFFRACTIONx_scangle_it3.212.5
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 (%)
1.5-1.570.3285129.60.32948240.0159263533657.6
1.57-1.650.28772210.30.28162780.0119113700076.8
1.65-1.750.27774390.26374970.019276824088.8
1.75-1.890.2598949.90.24481660.0099147906099
1.89-2.080.2549139.90.22382900.0089217920399.8
2.08-2.380.2298659.50.21582620.0089146912799.8
2.38-30.25197010.60.22481750.0089171914599.7
3-38.060.2048479.20.20883210.0079214916899.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2carbohydrate.paramcarbohydrate.top
X-RAY DIFFRACTION3water_rep.paramwater.top

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