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- PDB-1vdh: Structure-based functional identification of a novel heme-binding... -

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Basic information

Entry
Database: PDB / ID: 1vdh
TitleStructure-based functional identification of a novel heme-binding protein from thermus thermophilus HB8
Componentsmuconolactone isomerase-like protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / beta barrel / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


hydrogen peroxide-dependent heme synthase / heme biosynthetic process / peroxidase activity / heme binding / metal ion binding
Similarity search - Function
Apc35880; domain 1 / Coproheme decarboxylase / Heme-dependent peroxidase ChdC/CLD / Chlorite dismutase / Dimeric alpha-beta barrel / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Coproheme decarboxylase
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2 Å
AuthorsEbihara, A. / Okamoto, A. / Kousumi, Y. / Yamamoto, H. / Masui, R. / Ueyama, N. / Shibata, T. / Inoue, Y. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: J.STRUCT.FUNCT.GENOM. / Year: 2005
Title: Structure-based functional identification of a novel heme-binding protein from Thermus thermophilus HB8.
Authors: Ebihara, A. / Okamoto, A. / Kousumi, Y. / Yamamoto, H. / Masui, R. / Ueyama, N. / Yokoyama, S. / Kuramitsu, S.
History
DepositionMar 22, 2004Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 22, 2004Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 27, 2023Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: muconolactone isomerase-like protein
B: muconolactone isomerase-like protein
C: muconolactone isomerase-like protein
D: muconolactone isomerase-like protein
E: muconolactone isomerase-like protein


Theoretical massNumber of molelcules
Total (without water)144,7245
Polymers144,7245
Non-polymers00
Water18,3391018
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area17280 Å2
ΔGint-71 kcal/mol
Surface area47300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)99.738, 123.136, 131.439
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
muconolactone isomerase-like protein


Mass: 28944.758 Da / Num. of mol.: 5 / Mutation: K182E
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Plasmid: pET11a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q5SHL6
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 1018 / 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: 2.79 Å3/Da / Density % sol: 55.89 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.4
Details: 30% ethylene glycol, 0.1M sodium acetate, pH 4.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
Diffraction source
SourceSiteBeamlineIDWavelength (Å)Wavelength
SYNCHROTRONSPring-8 BL45XU10.9791, 0.9797, 1.020
SYNCHROTRONSPring-8 BL45XU20.98
Detector
TypeIDDetectorDate
RIGAKU JUPITER 2101CCDDec 3, 2001
RIGAKU RAXIS V2IMAGE PLATEJun 27, 2002
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1TRANSPARENT DIAMOND DOUBLE-CRYSTALMADMx-ray1
2TRANSPARENT DIAMOND DOUBLE-CRYSTALSINGLE WAVELENGTHMx-ray2
Radiation wavelength
IDWavelength (Å)Relative weight
10.97911
20.97971
31.021
40.981
ReflectionResolution: 2→50 Å / Num. all: 107812 / Num. obs: 107812 / % possible obs: 98.4 % / Redundancy: 4.9 % / Biso Wilson estimate: 15.5 Å2 / Rmerge(I) obs: 0.09 / Net I/σ(I): 15.7
Reflection shellResolution: 2→2.07 Å / Rmerge(I) obs: 0.165 / Mean I/σ(I) obs: 8.2 / Num. unique all: 10780 / % possible all: 99.6

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2→19.99 Å / Rfactor Rfree error: 0.002 / Data cutoff high absF: 3315974.62 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.218 10787 10 %RANDOM
Rwork0.188 ---
all0.192 ---
obs0.188 107633 98.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 19.4946 Å2 / ksol: 0.323262 e/Å3
Displacement parametersBiso mean: 15.7 Å2
Baniso -1Baniso -2Baniso -3
1--0.1 Å20 Å20 Å2
2---0.44 Å20 Å2
3---0.54 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.24 Å0.2 Å
Luzzati d res low-5 Å
Luzzati sigma a0.13 Å0.08 Å
Refinement stepCycle: LAST / Resolution: 2→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10150 0 0 1018 11168
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.2
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d24.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d1.06
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.151.5
X-RAY DIFFRACTIONc_mcangle_it1.652
X-RAY DIFFRACTIONc_scbond_it2.032
X-RAY DIFFRACTIONc_scangle_it3.022.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2→2.13 Å / Rfactor Rfree error: 0.005 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.225 1811 10.2 %
Rwork0.188 15903 -
obs--98 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP

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