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- PDB-3swj: Crystal structure of Campylobacter jejuni ChuZ -

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Basic information

Entry
Database: PDB / ID: 3swj
TitleCrystal structure of Campylobacter jejuni ChuZ
ComponentsPutative uncharacterized protein
KeywordsHEME BINDING PROTEIN / ChuZ / heme oxygenase / bacterial iron aquisition
Function / homology
Function and homology information


PNP-oxidase-like / Split barrel-like / Electron Transport, Fmn-binding Protein; Chain A / Pnp Oxidase; Chain A / Roll / Alpha-Beta Barrel / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
AZIDE ION / PROTOPORPHYRIN IX CONTAINING FE / :
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.409 Å
AuthorsHu, Y.
CitationJournal: Biochem.Biophys.Res.Commun. / Year: 2011
Title: Crystal structure of Campylobacter jejuni ChuZ: a split-barrel family heme oxygenase with a novel heme-binding mode.
Authors: Zhang, R. / Zhang, J. / Guo, G. / Mao, X. / Tong, W. / Zhang, Y. / Wang, D.C. / Hu, Y. / Zou, Q.
History
DepositionJul 14, 2011Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 9, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 10, 2013Group: Database references
Revision 1.2Mar 20, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)30,0184
Polymers28,7431
Non-polymers1,2753
Water30617
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Putative uncharacterized protein
hetero molecules

A: Putative uncharacterized protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)60,0358
Polymers57,4852
Non-polymers2,5506
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555x,-y,-z1
Buried area9520 Å2
ΔGint-95 kcal/mol
Surface area23040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)106.474, 106.698, 52.464
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-302-

HEM

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Components

#1: Protein Putative uncharacterized protein / ChuZ


Mass: 28742.531 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Strain: RM1221 / Gene: chuZ, CJE1785 / Plasmid: pET22b / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: Q5HSH8
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-AZI / AZIDE ION / Azide


Mass: 42.020 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: N3
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 2.7 Å3/Da / Density % sol: 53.2 %
Crystal growTemperature: 293 K / Method: microbatch / pH: 6.5
Details: 24% PEG 400, 0.1M MES, 0.1M imidazole, 5mM azide, pH 6.5, microbatch, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRF / Beamline: BL17U / Wavelength: 0.9794 Å
DetectorType: Mar225 / Detector: CCD / Date: Oct 31, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9794 Å / Relative weight: 1
ReflectionResolution: 2.4→74.978 Å / Num. all: 11858 / Num. obs: 11858 / % possible obs: 99.7 % / Redundancy: 5.3 % / Rsym value: 0.074 / Net I/σ(I): 12.4
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) allRmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRrim(I) allRsym valueNet I/σ(I) obs% possible all
2.4-2.535.30.5270.4731.6905017020.2260.5270.4733.399.9
2.53-2.685.30.3070.2752.7864716200.1320.3070.2754.899.9
2.68-2.875.30.1940.1754.3812415260.0830.1940.1757.199.9
2.87-3.15.30.1280.1166.2750814090.0540.1280.11610.199.9
3.1-3.395.30.0920.0838700313210.0380.0920.08314.199.8
3.39-3.795.30.0690.06210.2633211970.0280.0690.06218.799.9
3.79-4.385.20.0680.0629.1555710650.0280.0680.06221.2100
4.38-5.375.20.0840.0777.347339160.0340.0840.07722.8100
5.37-7.595.10.0690.0629.536307170.0290.0690.06221.999.9
7.59-42.8954.50.0420.03716.317403850.0190.0420.03723.793.5

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Phasing

PhasingMethod: molecular replacement

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.9data scaling
PHASER2.1.4phasing
PHENIX1.7_650refinement
PDB_EXTRACT3.1data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.409→37.407 Å / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.7661 / SU ML: 0.29 / σ(F): 1.33 / Phase error: 28.98 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2596 535 4.79 %
Rwork0.2064 --
obs0.2091 11177 93.67 %
Solvent computationShrinkage radii: 0.83 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 64.995 Å2 / ksol: 0.319 e/Å3
Displacement parametersBiso max: 186.4 Å2 / Biso mean: 87.0581 Å2 / Biso min: 28.79 Å2
Baniso -1Baniso -2Baniso -3
1-4.6226 Å2-0 Å2-0 Å2
2---2.2013 Å20 Å2
3----2.4213 Å2
Refinement stepCycle: LAST / Resolution: 2.409→37.407 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1959 0 79 17 2055
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.012087
X-RAY DIFFRACTIONf_angle_d1.0632834
X-RAY DIFFRACTIONf_chiral_restr0.077290
X-RAY DIFFRACTIONf_plane_restr0.002361
X-RAY DIFFRACTIONf_dihedral_angle_d19.815739
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 4

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.4091-2.65150.46021190.33952093221276
2.6515-3.0350.32611410.27532773291499
3.035-3.82320.30021330.218428452978100
3.8232-37.41110.20971420.174429313073100
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)
11.2812-0.40920.53951.4007-0.5751.4070.12160.2593-0.74970.08110.5594-1.25660.21240.34330.27650.57370.1085-0.19610.427-0.22471.29346.706-29.53052.2323
21.20560.1552-0.10993.56520.08941.4976-0.2159-0.25390.01471.26080.38880.39090.06660.0222-0.02220.48050.10170.08080.37720.01780.295430.73311.23279.4171
30.9521-0.26820.53340.0992-0.15550.31180.03360.20560.160.02110.05360.0645-0.01950.1772-0.0240.43830.0198-0.0940.48240.00950.669332.0006-18.42211.1346
40.0874-0.0004-0.00960.0235-0.00440.0121-0.0037-0.00920.0320.0132-0.0171-0.0099-0.02170.0047-0.00571.0471-0.0007-0.56021.0851-0.00530.933953.2349-28.95913.1285
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 2:83)
2X-RAY DIFFRACTION2(chain A and resid 84:251)
3X-RAY DIFFRACTION3(chain A and resid 300:301)
4X-RAY DIFFRACTION4(chain A and resid 302)

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