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- PDB-2ig3: Crystal structure of group III truncated hemoglobin from Campylob... -

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Basic information

Entry
Database: PDB / ID: 2ig3
TitleCrystal structure of group III truncated hemoglobin from Campylobacter jejuni
ComponentsGroup III truncated haemoglobin
KeywordsOxygen storage/transport / truncated hemoglobin / 2-on-2 globin / Oxygen storage-transport COMPLEX
Function / homology
Function and homology information


oxygen binding / heme binding / metal ion binding / cytoplasm
Similarity search - Function
Truncated hemoglobin / Bacterial-like globin / Globin/Protoglobin / Globins / Globin-like / Globin-like superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / CYANIDE ION / PROTOPORPHYRIN IX CONTAINING FE / Group 3 truncated hemoglobin ctb
Similarity search - Component
Biological speciesCampylobacter jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsNardini, M. / Pesce, A. / Labarre, M. / Ascenzi, P. / Guertin, M. / Bolognesi, M.
CitationJournal: J.Biol.Chem. / Year: 2006
Title: Structural determinants in the group III truncated hemoglobin from Campylobacter jejuni.
Authors: Nardini, M. / Pesce, A. / Labarre, M. / Richard, C. / Bolli, A. / Ascenzi, P. / Guertin, M. / Bolognesi, M.
History
DepositionSep 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 10, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.4Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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 / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _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_asym_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: Group III truncated haemoglobin
B: Group III truncated haemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,83113
Polymers29,9842
Non-polymers1,84611
Water1,65792
1
A: Group III truncated haemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)15,7905
Polymers14,9921
Non-polymers7984
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: Group III truncated haemoglobin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)16,0418
Polymers14,9921
Non-polymers1,0497
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5930 Å2
ΔGint-123 kcal/mol
Surface area13240 Å2
MethodPISA
Unit cell
Length a, b, c (Å)95.588, 95.588, 65.424
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein Group III truncated haemoglobin / Group III truncated hemoglobin


Mass: 14992.183 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni (Campylobacter) / Gene: ctb / Production host: Escherichia coli (E. coli) / References: UniProt: Q0PB48

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Non-polymers , 5 types, 103 molecules

#2: Chemical ChemComp-CYN / CYANIDE ION / Cyanide


Mass: 26.017 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: CN
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical
ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 92 / 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: 2.88 Å3/Da / Density % sol: 57.24 %
Crystal growTemperature: 277 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 2.0M Ammonium sulfate, 0.1M Sodium acetate, pH 5, VAPOR DIFFUSION, HANGING DROP, temperature 277K, pH 5.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.9537 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 15, 2006 / Details: cylindrical grazing incidence mirror
RadiationMonochromator: liquid nitrogen cooled channel-cut silicon monochromator
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9537 Å / Relative weight: 1
ReflectionResolution: 2.15→65.94 Å / Num. obs: 19090 / % possible obs: 100 % / Observed criterion σ(F): 1 / Observed criterion σ(I): 1 / Redundancy: 14.4 % / Biso Wilson estimate: 37.6 Å2 / Rmerge(I) obs: 0.067 / Rsym value: 0.067 / Net I/σ(I): 30.4
Reflection shellResolution: 2.15→2.27 Å / Redundancy: 14.8 % / Rmerge(I) obs: 0.313 / Mean I/σ(I) obs: 8.9 / Num. unique all: 2754 / Rsym value: 0.313 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0005refinement
ProDCdata collection
MOSFLMdata reduction
CCP4(SCALA)data scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1UX8

1ux8


Resolution: 2.15→31.3 Å / Cor.coef. Fo:Fc: 0.941 / Cor.coef. Fo:Fc free: 0.913 / SU B: 5.281 / SU ML: 0.14 / Cross valid method: THROUGHOUT / ESU R: 0.249 / ESU R Free: 0.215 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.262 1934 10.1 %RANDOM
Rwork0.20593 ---
obs0.21154 17121 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 35.224 Å2
Refinement stepCycle: LAST / Resolution: 2.15→31.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2094 0 122 92 2308
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.010.0222283
X-RAY DIFFRACTIONr_angle_refined_deg1.132.0773094
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.855249
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.2825.614114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.39615408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.204154
X-RAY DIFFRACTIONr_chiral_restr0.0860.2290
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.021742
X-RAY DIFFRACTIONr_nbd_refined0.1960.21096
X-RAY DIFFRACTIONr_nbtor_refined0.30.21511
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1290.289
X-RAY DIFFRACTIONr_metal_ion_refined0.0120.21
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2770.243
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1520.28
X-RAY DIFFRACTIONr_mcbond_it0.7371.51310
X-RAY DIFFRACTIONr_mcangle_it1.26522011
X-RAY DIFFRACTIONr_scbond_it1.76831147
X-RAY DIFFRACTIONr_scangle_it2.7484.51079
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.306 148 -
Rwork0.232 1238 -
obs--100 %

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