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- PDB-2cn4: The crystal structure of the secreted dimeric form of the hemopho... -

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Basic information

Entry
Database: PDB / ID: 2cn4
TitleThe crystal structure of the secreted dimeric form of the hemophore HasA reveals a domain swapping with an exchanged heme ligand
ComponentsHEMOPHORE HASA
KeywordsTRANSPORT PROTEIN / DOMAIN SWAPPING / HEME / IRON / DIMERIC FORM / METAL-BINDING
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 / PHOSPHATE ION / Hemophore HasA
Similarity search - Component
Biological speciesSERRATIA MARCESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.3 Å
AuthorsCzjzek, M. / Letoffe, S. / Wandersman, C. / Delepierre, M. / Lecroisey, A. / Izadi-Pruneyre, N.
CitationJournal: J.Mol.Biol. / Year: 2007
Title: The Crystal Structure of the Secreted Dimeric Form of the Hemophore Hasa Reveals a Domain Swapping with an Exchanged Heme Ligand
Authors: Czjzek, M. / Letoffe, S. / Wandersman, C. / Delepierre, M. / Lecroisey, A. / Izadi-Pruneyre, N.
History
DepositionMay 18, 2006Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 26, 2006Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_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.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_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.ptnr2_auth_asym_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
Remark 700 SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN ... SHEET THE SHEET STRUCTURE OF THIS MOLECULE IS BIFURCATED. IN ORDER TO REPRESENT THIS FEATURE IN THE SHEET RECORDS BELOW, TWO SHEETS ARE DEFINED.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: HEMOPHORE HASA
B: HEMOPHORE HASA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9596
Polymers35,5362
Non-polymers1,4234
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)47.080, 62.320, 56.820
Angle α, β, γ (deg.)90.00, 105.34, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A2 - 201
2115B2 - 201

NCS oper: (Code: given
Matrix: (-1, -0.0007, -0.0013), (-0.001, 0.9796, 0.201), (0.0011, 0.201, -0.9796)
Vector: -36.0933, 1.4499, -14.1739)

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Components

#1: Protein HEMOPHORE HASA / HEME BINDING PROTEIN HASA / HEME ACQUISITION SYSTEM PROTEIN A


Mass: 17767.902 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: H32A, Y75B, H32B AND Y75A ARE LIGANDS TO THE HEME IRONS HEM200A AND HEM200B RESPECTIVELY
Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Cell: SECRETED / Plasmid: PSYC34PAM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): STRAIN POP3 / References: UniProt: Q54450
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical ChemComp-PO4 / PHOSPHATE ION


Mass: 94.971 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: PO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Compound detailsIT IS CAPABLE OF BINDING FREE HEME AS WELL AS CAN ACQUIRE IT FROM THE HEMOGLOBIN.IT IS REPONSIBLE ...IT IS CAPABLE OF BINDING FREE HEME AS WELL AS CAN ACQUIRE IT FROM THE HEMOGLOBIN.IT IS REPONSIBLE FOR TRANSFERRING HEME FROM HEMOGLOB TO THE HASR RECEPTOR WHICH RELEASES IT INTO THE BACTERIUM.

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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: 2.17 Å3/Da / Density % sol: 43 %
Crystal growpH: 8.5
Details: 2 MICROLITERS PROTEIN (AT A CONCENTRATION OF ABOUT 4 MG/ML) WERE MIXED WITH 1 MICROLITER RESERVOIR CONSISTING OF 100 MM TRIS BUFFER AT PH 8.5, 2 M K2HPO4 AND 2 M NAH2PO4.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979
DetectorType: MARRESEARCH / Detector: CCD / Date: Oct 4, 2004
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.3→55 Å / Num. obs: 14221 / % possible obs: 95.8 % / Redundancy: 1.9 % / Rmerge(I) obs: 0.03 / Net I/σ(I): 18
Reflection shellResolution: 2.3→2.38 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.07 / Mean I/σ(I) obs: 7 / % possible all: 91.1

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Processing

Software
NameVersionClassification
REFMAC5.1.24refinement
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1B2V

1b2v


Resolution: 2.3→30 Å / Cor.coef. Fo:Fc: 0.939 / Cor.coef. Fo:Fc free: 0.889 / SU B: 4.185 / SU ML: 0.105 / Cross valid method: THROUGHOUT / ESU R: 0.492 / ESU R Free: 0.246 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.224 676 5 %RANDOM
Rwork0.169 ---
obs0.172 12866 95.3 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 14.9 Å2
Baniso -1Baniso -2Baniso -3
1--0.6 Å20 Å20.53 Å2
2--0.4 Å20 Å2
3---0.48 Å2
Refinement stepCycle: LAST / Resolution: 2.3→30 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2512 0 96 149 2757
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0212676
X-RAY DIFFRACTIONr_bond_other_d0.0020.022156
X-RAY DIFFRACTIONr_angle_refined_deg1.2012.0263680
X-RAY DIFFRACTIONr_angle_other_deg0.80135002
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8145344
X-RAY DIFFRACTIONr_dihedral_angle_2_deg
X-RAY DIFFRACTIONr_dihedral_angle_3_deg
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0730.2386
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.023148
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02538
X-RAY DIFFRACTIONr_nbd_refined0.1920.2560
X-RAY DIFFRACTIONr_nbd_other0.2360.22460
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0820.21352
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1750.298
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1580.216
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2320.226
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1390.212
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4061.51682
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.80122654
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.3173994
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it2.1584.51026
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Auth asym-ID: A / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

NumberTypeRms dev position (Å)Weight position
1008medium positional0.120.5
1374loose positional0.345
1008medium thermal0.362
1374loose thermal0.7410
LS refinement shellResolution: 2.3→2.36 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.231 39
Rwork0.179 898

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