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- PDB-2g5g: Cofacial heme binding to ChaN of Campylobacter jejuni -

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Basic information

Entry
Database: PDB / ID: 2g5g
TitleCofacial heme binding to ChaN of Campylobacter jejuni
Componentsputative lipoprotein
KeywordsTRANSPORT PROTEIN / cofacial heme / tyrosine ligand / dimer
Function / homology
Function and homology information


Haem-binding uptake, Tiki superfamily, ChaN, domain 2 / Haem-binding uptake, Tiki superfamily, ChaN / Ferric uptake regulator, CjrA, predicted / Haem-binding uptake, Tiki superfamily, ChaN / Rossmann fold - #11550 / Helicase, Ruva Protein; domain 3 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / : / Putative iron transport protein
Similarity search - Component
Biological speciesCampylobacter jejuni subsp. jejuni (Campylobacter)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.9 Å
AuthorsChan, A.C. / Murphy, M.E.
CitationJournal: J.Mol.Biol. / Year: 2006
Title: Cofacial Heme Binding is Linked to Dimerization by a Bacterial Heme Transport Protein.
Authors: Chan, A.C. / Lelj-Garolla, B. / Rosell, F.I. / Pedersen, K.A. / Mauk, A.G. / Murphy, M.E.
History
DepositionFeb 22, 2006Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 3, 2006Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Oct 18, 2017Group: Refinement description / Category: software
Item: _software.classification / _software.contact_author ..._software.classification / _software.contact_author / _software.contact_author_email / _software.date / _software.language / _software.location / _software.name / _software.type / _software.version

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
X: putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,5982
Polymers30,9821
Non-polymers6161
Water4,378243
1
X: putative lipoprotein
hetero molecules

X: putative lipoprotein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)63,1974
Polymers61,9642
Non-polymers1,2332
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_657-x+1,y,-z+21
Unit cell
Length a, b, c (Å)87.918, 58.790, 82.395
Angle α, β, γ (deg.)90.00, 119.21, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein putative lipoprotein


Mass: 30981.945 Da / Num. of mol.: 1 / Fragment: soluble domain (residues 20-283)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Campylobacter jejuni subsp. jejuni (Campylobacter)
Species: Campylobacter jejuni / Strain: NCTC 11168 / Gene: CJ0177 / Plasmid: pET28a / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: GenBank: 6967670, UniProt: Q0PBW2*PLUS
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 243 / 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: 3 Å3/Da / Density % sol: 58.99 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 15% PEG 4000, 100 mM HEPES, pH 7.0, vapor diffusion, hanging drop, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL1-5 / Wavelength: 0.978726 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Apr 8, 2005
Details: 2-crystal monochromator, Si111, 1m long Rh coated bent cylindrical mirror for horizontal and vertical focussing
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.978726 Å / Relative weight: 1
ReflectionResolution: 1.9→36 Å / Num. all: 28754 / Num. obs: 28754 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 3.48 % / Rmerge(I) obs: 0.084 / Net I/σ(I): 8.638
Reflection shellResolution: 1.9→1.97 Å / Rmerge(I) obs: 0.333 / Mean I/σ(I) obs: 2.699 / % possible all: 97.9

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Phasing

PhasingMethod: SAD
Phasing MADD res high: 2 Å / D res low: 50 Å / FOM : 0.3 / Reflection: 24052
Phasing MAD set site
IDCartn x (Å)Cartn y (Å)Cartn z (Å)Atom type symbolB isoOccupancy
14.0060.1918.281SE34.81.33
212.07511.06232.413SE22.10.93
311.9051.79916.34SE38.20.8
420.99812.10827.775SE52.50.72
Phasing MAD shell
Resolution (Å)FOM Reflection
7.26-500.461158
4.56-7.260.432025
3.56-4.560.412593
3.02-3.560.383033
2.66-3.020.333389
2.41-2.660.293719
2.22-2.410.213984
2.06-2.220.154151
Phasing dmFOM : 0.61 / FOM acentric: 0.61 / FOM centric: 0.59 / Reflection: 24053 / Reflection acentric: 23062 / Reflection centric: 991
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
5.7-35.5560.930.940.821100961139
3.6-5.70.930.940.8433153088227
2.9-3.60.830.830.741253937188
2.5-2.90.660.660.4641163960156
2.1-2.50.460.460.3371076909198
2-2.10.270.280.144290420783

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
RESOLVE2.08phasing
REFMAC5.2.0005refinement
PDB_EXTRACT1.701data extraction
HKL-2000data reduction
RefinementMethod to determine structure: SAD / Resolution: 1.9→36 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.936 / SU B: 3.669 / SU ML: 0.108 / Isotropic thermal model: isotropic / Cross valid method: THROUGHOUT / ESU R: 0.146 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.24172 1469 5.1 %RANDOM
Rwork0.20718 ---
obs0.20902 27276 98.97 %-
all-28745 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 33.982 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20 Å21.03 Å2
2---1.2 Å20 Å2
3---1.02 Å2
Refinement stepCycle: LAST / Resolution: 1.9→36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2072 0 43 243 2358
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0222159
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.4372.0212922
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.1975254
X-RAY DIFFRACTIONr_dihedral_angle_2_deg39.66526.18697
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.15815420
X-RAY DIFFRACTIONr_dihedral_angle_4_deg6.603153
X-RAY DIFFRACTIONr_chiral_restr0.1090.2325
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021565
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2040.21034
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.2980.21482
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1870.2211
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2310.248
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2890.214
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.0171.51310
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.55622058
X-RAY DIFFRACTIONr_scbond_it2.2513964
X-RAY DIFFRACTIONr_scangle_it3.2774.5862
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.9→1.949 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.341 103 -
Rwork0.276 1950 -
obs--97.67 %

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