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- PDB-1b2v: HEME-BINDING PROTEIN A -

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Basic information

Entry
Database: PDB / ID: 1b2v
TitleHEME-BINDING PROTEIN A
ComponentsPROTEIN (HEME-BINDING PROTEIN A)
KeywordsTRANSPORT PROTEIN / HEME ACQUISITION / IRON METABOLISM
Function / homology
Function and homology information


extracellular region / metal ion binding
Similarity search - Function
Heme-binding Protein A; Chain: A; / Haem-binding HasA / Haem-binding HasA / Haem-binding HasA superfamily / Heme-binding protein A (HasA) / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PROTOPORPHYRIN IX CONTAINING FE / Hemophore HasA
Similarity search - Component
Biological speciesSerratia marcescens (bacteria)
MethodX-RAY DIFFRACTION / MIRAS / Resolution: 1.9 Å
AuthorsArnoux, P. / Haser, R. / Izadi, N. / Lecroisey, A. / Wandersma, N.C. / Czjzek, M.
Citation
Journal: Nat.Struct.Biol. / Year: 1999
Title: The crystal structure of HasA, a hemophore secreted by Serratia marcescens.
Authors: Arnoux, P. / Haser, R. / Izadi, N. / Lecroisey, A. / Delepierre, M. / Wandersman, C. / Czjzek, M.
#1: Journal: Proc.Natl.Acad.Sci.USA / Year: 1994
Title: Iron acquisition from heme and hemoglobin by a Serratia marcescens extracellular protein.
Authors: Letoffe, S. / Ghigo, J.M. / Wandersman, C.
History
DepositionDec 1, 1998Deposition site: PDBE / Processing site: RCSB
Revision 1.0Jun 24, 1999Provider: repository / Type: Initial release
Revision 1.1Oct 16, 2007Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Nov 12, 2014Group: Database references / Derived calculations
Revision 1.4Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_alt_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_alt_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_ptnr2_label_alt_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.ptnr1_symmetry / _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_conn.ptnr2_symmetry / _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: PROTEIN (HEME-BINDING PROTEIN A)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9453
Polymers19,2891
Non-polymers6572
Water3,171176
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)41.650, 80.660, 63.230
Angle α, β, γ (deg.)90.00, 93.58, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein PROTEIN (HEME-BINDING PROTEIN A) / HASA


Mass: 19288.639 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Cellular location: EXTRACELLULARGlossary of biology / Production host: Escherichia coli (E. coli) / References: UniProt: Q54450
#2: Chemical ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Ca
#3: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


Mass: 18.015 Da / Num. of mol.: 176 / 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: 2.75 Å3/Da / Density % sol: 55.23 %
Crystal growpH: 4.6 / Details: 0.2M CACL, 0.1M NA ACETATE PH 4.6, 20% ISOPRPANOL
Components of the solutions
IDNameCrystal-IDSol-ID
10.2M CACL12
20.1M NA ACETATE PH 4.612
320% ISOPRPANOL12
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Details: drop consists of equal volume of protein and reservoir solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18.7 mg/mlprotein1drop
2100 mM1dropNaCl
3100 mMTris-HCl1drop
40.2 Mcalcium chloride1reservoir
50.1 Msodium acetate1reservoir
620 %isopropanol1reservoir

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Data collection

DiffractionMean temperature: 288 K
Diffraction sourceWavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: May 15, 1998
RadiationMonochromator: GRAPHITE CRYSTAL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.9→20 Å / Num. obs: 61510 / % possible obs: 95.2 % / Redundancy: 2.5 % / Biso Wilson estimate: 30.96 Å2 / Rsym value: 7.9 / Net I/σ(I): 13.9
Reflection shellResolution: 1.9→1.97 Å / Redundancy: 1.4 % / Mean I/σ(I) obs: 2.5 / Rsym value: 29 / % possible all: 94.2
Reflection
*PLUS
Num. obs: 15800 / Num. measured all: 61510 / Rmerge(I) obs: 0.079
Reflection shell
*PLUS
% possible obs: 94.2 % / Rmerge(I) obs: 0.29

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Processing

Software
NameVersionClassification
REFMACrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIRAS / Resolution: 1.9→15 Å / SU B: 3.49 / SU ML: 0.12 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.18 / ESU R Free: 0.15 / Details: ALTERNATIVE CONFORMATION FOR THE B TYPE HEME
RfactorNum. reflection% reflectionSelection details
Rfree0.218 775 5 %RANDOM
Rwork0.175 ---
obs0.177 15496 95.2 %-
Displacement parametersBiso mean: 24.6 Å2
Refinement stepCycle: LAST / Resolution: 1.9→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1256 0 44 176 1476
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.014
X-RAY DIFFRACTIONp_angle_d2.37
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor

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