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- PDB-2wy4: Structure of bacterial globin from Campylobacter jejuni at 1.35 A... -

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Basic information

Entry
Database: PDB / ID: 2wy4
TitleStructure of bacterial globin from Campylobacter jejuni at 1.35 A resolution
ComponentsSINGLE DOMAIN HAEMOGLOBIN
KeywordsOXYGEN TRANSPORT / HEME / TRANSPORT
Function / homology
Function and homology information


nitric oxide dioxygenase NAD(P)H activity / cellular response to nitrosative stress / nitric oxide catabolic process / FAD binding / oxygen carrier activity / oxygen binding / heme binding / metal ion binding
Similarity search - Function
Globin/Protoglobin / Globins / Globin domain profile. / Globin-like / Globin / Globin / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Single domain haemoglobin
Similarity search - Component
Biological speciesCAMPYLOBACTER JEJUNI (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.35 Å
AuthorsBarynin, V.V. / Sedelnikova, S.E. / Shepherd, M. / Wu, G. / Poole, R.K. / Rice, D.W.
CitationJournal: J.Biol.Chem. / Year: 2010
Title: The Single-Domain Globin from the Pathogenic Bacterium Campylobacter Jejuni: Novel D-Helix Conformation, Proximal Hydrogen Bonding that Influences Ligand Binding, and Peroxidase-Like Redox Properties.
Authors: Shepherd, M. / Barynin, V.V. / Lu, C. / Bernhardt, P.V. / Wu, G. / Yeh, S.R. / Egawa, T. / Sedelnikova, S.E. / Rice, D.W. / Wilson, J.L. / Poole, R.K.
History
DepositionNov 11, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 16, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _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

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Assembly

Deposited unit
A: SINGLE DOMAIN HAEMOGLOBIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,7453
Polymers16,1031
Non-polymers6432
Water2,648147
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)39.550, 37.980, 43.760
Angle α, β, γ (deg.)90.00, 102.68, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein SINGLE DOMAIN HAEMOGLOBIN


Mass: 16102.892 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: CN / Source: (gene. exp.) CAMPYLOBACTER JEJUNI (Campylobacter) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: Q0P842
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-CYN / CYANIDE ION


Mass: 26.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CN
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 147 / 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: 1.99 Å3/Da / Density % sol: 38.22 % / Description: NONE
Crystal growpH: 8 / Details: 1.8M A.S.,0.1M TRIS/HCL, PH8.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX14.2 / Wavelength: 0.978
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978 Å / Relative weight: 1
ReflectionResolution: 1.35→19.3 Å / Num. obs: 24978 / % possible obs: 95 % / Observed criterion σ(I): 1 / Redundancy: 2 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 11.7
Reflection shellResolution: 1.35→1.37 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.45 / Mean I/σ(I) obs: 2.1 / % possible all: 89

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Processing

Software
NameVersionClassification
REFMAC5refinement
DENZOdata reduction
SCALEPACKdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1VHB

1vhb


Resolution: 1.35→20 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.957 / SU B: 2.878 / SU ML: 0.062 / Cross valid method: THROUGHOUT / ESU R: 0.08 / ESU R Free: 0.068 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.20887 1567 5.9 %RANDOM
Rwork0.17808 ---
obs0.17997 24978 94.79 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 15.441 Å2
Baniso -1Baniso -2Baniso -3
1--1.17 Å20 Å20.37 Å2
2---0.81 Å20 Å2
3---2.14 Å2
Refinement stepCycle: LAST / Resolution: 1.35→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1118 0 45 147 1310
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0221219
X-RAY DIFFRACTIONr_bond_other_d0.0010.021122
X-RAY DIFFRACTIONr_angle_refined_deg1.4532.0891652
X-RAY DIFFRACTIONr_angle_other_deg0.82332649
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.4793138
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.89215246
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.2178
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021274
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02194
X-RAY DIFFRACTIONr_nbd_refined0.2540.3316
X-RAY DIFFRACTIONr_nbd_other0.1890.31105
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.584
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.3470.316
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2540.342
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2060.530
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.4871.5701
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it2.12221144
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it2.9213518
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it4.1094.5508
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr1.30121219
X-RAY DIFFRACTIONr_sphericity_free10.825149
X-RAY DIFFRACTIONr_sphericity_bonded651191
LS refinement shellResolution: 1.35→1.373 Å / Total num. of bins used: 30
RfactorNum. reflection% reflection
Rfree0.317 71 -
Rwork0.279 1147 -
obs--85.2 %

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