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- PDB-2rg7: Apo- Crystal Structure of a Periplasmic Heme Binding Protein from... -

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Basic information

Entry
Database: PDB / ID: 2rg7
TitleApo- Crystal Structure of a Periplasmic Heme Binding Protein from Shigella dysenteriae
ComponentsPeriplasmic HEME binding protein
KeywordsTRANSPORT PROTEIN / PERIPLASMIC HEME BINDING PROTEIN
Function / homology
Function and homology information


: / ABC transporter periplasmic binding domain / Periplasmic binding protein / Iron siderophore/cobalamin periplasmic-binding domain profile. / Nitrogenase molybdenum iron protein domain / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Periplasmic binding protein
Similarity search - Component
Biological speciesShigella dysenteriae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.05 Å
AuthorsHo, W.W. / Li, H.
CitationJournal: J.Biol.Chem. / Year: 2007
Title: Holo- and apo-bound structures of bacterial periplasmic heme-binding proteins.
Authors: Ho, W.W. / Li, H. / Eakanunkul, S. / Tong, Y. / Wilks, A. / Guo, M. / Poulos, T.L.
History
DepositionOct 2, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Aug 30, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
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: Periplasmic HEME binding protein
B: Periplasmic HEME binding protein
C: Periplasmic HEME binding protein
D: Periplasmic HEME binding protein


Theoretical massNumber of molelcules
Total (without water)110,3304
Polymers110,3304
Non-polymers00
Water4,432246
1
A: Periplasmic HEME binding protein
C: Periplasmic HEME binding protein


Theoretical massNumber of molelcules
Total (without water)55,1652
Polymers55,1652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2180 Å2
ΔGint-11 kcal/mol
Surface area22640 Å2
MethodPISA
2
B: Periplasmic HEME binding protein
D: Periplasmic HEME binding protein


Theoretical massNumber of molelcules
Total (without water)55,1652
Polymers55,1652
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2190 Å2
ΔGint-10 kcal/mol
Surface area22550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.817, 73.280, 72.380
Angle α, β, γ (deg.)71.44, 77.80, 89.90
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Periplasmic HEME binding protein


Mass: 27582.484 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Shigella dysenteriae (bacteria) / Plasmid: pSHU262 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21-DE3 / References: UniProt: O70018
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 246 / 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: 2.44 Å3/Da / Density % sol: 49.53 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1m SODIUM CITRATE, 0.05m AMMONIUM BROMIDE, 15% POLYETHYLENE GLYCOL 4000, pH 4.0, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 1 Å
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Jun 2, 2006 / Details: mirrors
RadiationMonochromator: GRAPHITE / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.05→35.9 Å / Num. obs: 63384 / % possible obs: 98 % / Observed criterion σ(F): 2 / Redundancy: 3.9 % / Biso Wilson estimate: 27.1 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 27.19
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 3.9 % / Rmerge(I) obs: 0.666 / Mean I/σ(I) obs: 2.01 / Rsym value: 0.666 / % possible all: 97

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 2R7A

2r7a


Resolution: 2.05→35.9 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1039732.75 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.274 6402 10.1 %RANDOM
Rwork0.232 ---
obs0.232 63380 97.4 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 65.7671 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 48.1 Å2
Baniso -1Baniso -2Baniso -3
1--9.49 Å2-6.66 Å2-3.97 Å2
2---0.9 Å27.82 Å2
3---10.39 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.36 Å0.29 Å
Luzzati d res low-5 Å
Luzzati sigma a0.34 Å0.31 Å
Refinement stepCycle: LAST / Resolution: 2.05→35.9 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7736 0 0 246 7982
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_d21.9
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.85
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.491.5
X-RAY DIFFRACTIONc_mcangle_it2.392
X-RAY DIFFRACTIONc_scbond_it2.222
X-RAY DIFFRACTIONc_scangle_it3.242.5
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.343 1028 10.3 %
Rwork0.311 8973 -
obs--91.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2param19x.heme2water.top
X-RAY DIFFRACTION3water_rep.paramtoph19x.heme2
X-RAY DIFFRACTION4hetero.parhetero.top

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