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- PDB-2r7a: Crystal Structure of a Periplasmic Heme Binding Protein from Shig... -

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Basic information

Entry
Database: PDB / ID: 2r7a
TitleCrystal Structure of a Periplasmic Heme Binding Protein from Shigella dysenteriae
ComponentsBacterial heme binding protein
KeywordsTRANSPORT PROTEIN / periplasmic binding protein / heme transport
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
PROTOPORPHYRIN IX CONTAINING FE / 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. / Poulos, T.L.
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
DepositionSep 7, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 9, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Apr 16, 2014Group: Data collection
Revision 1.3Aug 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_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

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Assembly

Deposited unit
A: Bacterial heme binding protein
B: Bacterial heme binding protein
C: Bacterial heme binding protein
D: Bacterial heme binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,9465
Polymers110,3304
Non-polymers6161
Water8,989499
1
A: Bacterial heme binding protein
C: Bacterial heme binding protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)55,7813
Polymers55,1652
Non-polymers6161
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3360 Å2
ΔGint-30 kcal/mol
Surface area22260 Å2
MethodPISA
2
B: Bacterial heme binding protein
D: Bacterial 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-11 kcal/mol
Surface area22800 Å2
MethodPISA
Unit cell
Length a, b, c (Å)54.700, 73.308, 73.316
Angle α, β, γ (deg.)70.25, 79.02, 90.22
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Bacterial 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) / Strain: pSHU262 / Plasmid: pSHU262 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: O70018
#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.: 499 / 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: 2.46 Å3/Da / Density % sol: 49.93 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 4
Details: 0.1M sodium citrate, 0.05M ammonium bromide, 15% polyethylene glycol 4000, 0.001M hemin chloride, 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 6, 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→43.86 Å / Num. obs: 63384 / % possible obs: 98 % / Observed criterion σ(I): -3 / Redundancy: 3.9 % / Biso Wilson estimate: 19.7 Å2 / Rmerge(I) obs: 0.057 / Rsym value: 0.057 / Net I/σ(I): 27.2
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 3.9 % / Mean I/σ(I) obs: 2.01 / Rsym value: 0.67 / % possible all: 97

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Processing

Software
NameVersionClassification
CNS1.2refinement
HKL-2000data collection
HKL-2000data reduction
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: model of PhuT, PDB ENTRY 2R79

2r79


Resolution: 2.05→43.86 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 1452602.24 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber / Details: BULK SOLVENT MODEL USED
RfactorNum. reflection% reflectionSelection details
Rfree0.255 6415 10.1 %RANDOM
Rwork0.21 ---
obs0.21 63591 96.5 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 66.0413 Å2 / ksol: 0.4 e/Å3
Displacement parametersBiso mean: 39 Å2
Baniso -1Baniso -2Baniso -3
1--5.5 Å2-6.06 Å2-4.81 Å2
2--0.95 Å25.26 Å2
3---4.55 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.31 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.26 Å0.2 Å
Refinement stepCycle: LAST / Resolution: 2.05→43.86 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7741 0 43 499 8283
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_d22.1
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.92
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.441.5
X-RAY DIFFRACTIONc_mcangle_it2.252
X-RAY DIFFRACTIONc_scbond_it2.312
X-RAY DIFFRACTIONc_scangle_it3.382.5
LS refinement shellResolution: 2.05→2.18 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.302 1111 10.7 %
Rwork0.26 9236 -
obs--94 %
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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