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- PDB-1dk0: CRYSTAL STRUCTURE OF THE HEMOPHORE HASA FROM SERRATIA MARCESCENS ... -

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Basic information

Entry
Database: PDB / ID: 1dk0
TitleCRYSTAL STRUCTURE OF THE HEMOPHORE HASA FROM SERRATIA MARCESCENS CRYSTAL FORM P2(1), PH8
ComponentsHEME-BINDING PROTEIN A
KeywordsTRANSPORT PROTEIN / PROTEIN-HEME COMPLEX / TWO HEME INSERTIONS
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 / Resolution: 1.77 Å
AuthorsArnoux, P. / Haser, R. / Izadi-Pruneyre, N. / Lecroisey, A. / Czjzek, M.
Citation
Journal: Proteins / Year: 2000
Title: Functional aspects of the heme bound hemophore HasA by structural analysis of various crystal forms.
Authors: Arnoux, P. / Haser, R. / Izadi-Pruneyre, N. / Lecroisey, A. / Czjzek, M.
#1: 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.
History
DepositionDec 6, 1999Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 27, 2000Provider: repository / Type: Initial release
Revision 1.1Apr 27, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 7, 2024Group: 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_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.pdbx_dist_value / _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_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
Remark 300BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 ...BIOMOLECULE: 1, 2 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). Biological assembly is a monomer. The other monomer in the AU probably does not have biological significance.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEME-BINDING PROTEIN A
B: HEME-BINDING PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8104
Polymers38,5772
Non-polymers1,2332
Water3,999222
1
A: HEME-BINDING PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9052
Polymers19,2891
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: HEME-BINDING PROTEIN A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,9052
Polymers19,2891
Non-polymers6161
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)45.540, 66.210, 58.930
Angle α, β, γ (deg.)90.00, 104.91, 90.00
Int Tables number4
Space group name H-MP1211
DetailsBiological assembly is a monomer. The other monomer in the AU probably does not have biological significance.

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Components

#1: Protein HEME-BINDING PROTEIN A / HASA


Mass: 19288.639 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Serratia marcescens (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q54450
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME / Heme B


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


Mass: 18.015 Da / Num. of mol.: 222 / 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: 2.22 Å3/Da / Density % sol: 44.72 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 8
Details: 0.1M NaHepes, pH8.0, 1.4M NaKTartrate, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.5 / Details: Arnoux, P., (1999) Nat.Struct.Biol., 6, 516.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
115 mg/mlprotein1dropsaturated in heme
2100 mMcacodylate1reservoir
3140 mMzinc acetate dihydrate1reservoir
42 %glycerol1reservoir
59-11 %PEG80001reservoir

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Data collection

DiffractionMean temperature: 298 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU RU200 / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Feb 1, 1999
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.77→20 Å / Num. all: 31089 / Num. obs: 31089 / % possible obs: 94.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5 % / Biso Wilson estimate: 14.7 Å2 / Rmerge(I) obs: 0.063 / Net I/σ(I): 8.3
Reflection shellResolution: 1.77→1.82 Å / Redundancy: 2.3 % / Rmerge(I) obs: 0.371 / % possible all: 89.3
Reflection shell
*PLUS
% possible obs: 89.3 % / Mean I/σ(I) obs: 2

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Processing

Software
NameVersionClassification
AMoREphasing
REFMACrefinement
DENZOdata reduction
CCP4(SCALA)data scaling
RefinementResolution: 1.77→15 Å / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflectionSelection details
Rfree0.213 1569 5% Random
Rwork0.169 --
all0.175 31059 -
obs0.175 29490 -
Refinement stepCycle: LAST / Resolution: 1.77→15 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2512 0 86 222 2820
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.018
X-RAY DIFFRACTIONp_angle_d2.4
Software
*PLUS
Name: REFMAC / Classification: refinement
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_angle_d
X-RAY DIFFRACTIONp_angle_deg2.4

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