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- PDB-2uyd: Crystal structure of the SmHasA mutant H83A -

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Basic information

Entry
Database: PDB / ID: 2uyd
TitleCrystal structure of the SmHasA mutant H83A
ComponentsHEMOPHORE HASA
KeywordsMETAL BINDING PROTEIN / HEME / IRON / HEMOPHORE / HEME BINDING / IRON LIGATION / METAL-BINDING / HEME ACQUISITION SYSTEM / METAL-BINDING PROTEIN
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
ACETATE ION / PROTOPORPHYRIN IX CONTAINING FE / Hemophore HasA
Similarity search - Component
Biological speciesSERRATIA MARCESCENS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsCzjzek, M. / Caillet-Saguy, C. / Fournelle, A. / Guigliarelli, B. / Izadi-Pruneyre, N. / Lecroisey, A.
CitationJournal: J.Biol.Chem. / Year: 2008
Title: Deciphering the Structural Role of Histidine 83 for Heme Binding in Hemophore Hasa.
Authors: Caillet-Saguy, C. / Turano, P. / Piccioli, M. / Lukat-Rodgers, G.S. / Czjzek, M. / Guigliarelli, B. / Izadi-Pruneyre, N. / Rodgers, K.R. / Delepierre, M. / Lecroisey, A.
History
DepositionApr 4, 2007Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 25, 2007Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 8, 2019Group: Data collection / Experimental preparation / Other
Category: exptl_crystal_grow / pdbx_database_proc / pdbx_database_status
Item: _exptl_crystal_grow.temp / _pdbx_database_status.recvd_author_approval
Revision 1.4Dec 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 / struct_site
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_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.ptnr2_auth_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_alt_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _pdbx_struct_conn_angle.ptnr2_label_atom_id / _pdbx_struct_conn_angle.ptnr2_label_comp_id / _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_ptnr1_label_alt_id / _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

Downloads & links

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Assembly

Deposited unit
X: HEMOPHORE HASA
hetero molecules


Theoretical massNumber of molelcules
Total (without water)20,47912
Polymers19,2221
Non-polymers1,25811
Water1,22568
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
Unit cell
Length a, b, c (Å)110.670, 110.670, 52.355
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 19221.570 Da / Num. of mol.: 1 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: HEME BOUND BY TWO AXIAL LIGANDS, HISTIDINE 32 AND TYROSINE 75
Source: (gene. exp.) SERRATIA MARCESCENS (bacteria) / Strain: SM365 / Plasmid: PSYC34PAM / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): POP3 / References: UniProt: Q54450
#2: Chemical ChemComp-HEM / PROTOPORPHYRIN IX CONTAINING FE / HEME


Mass: 616.487 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C34H32FeN4O4
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 68 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN X, HIS 83 TO ALA CONVEYS HEME FROM HEMOGLOBIN TO THE HASR RECEPTOR ...ENGINEERED RESIDUE IN CHAIN X, HIS 83 TO ALA CONVEYS HEME FROM HEMOGLOBIN TO THE HASR RECEPTOR WHICH RELEASES IT INTO THE BACTERIUM
Sequence detailsMUTANT WITH H83A REPLACEMENT

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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: 5 Å3/Da / Density % sol: 75.5 % / Description: NONE
Crystal growTemperature: 293 K / pH: 6.5
Details: DROPS WERE PREPARED BY MIXING 2MICROL OF THE PROTEIN SOLUTION WITH 1 MICROL OF THE RESERVOIR SOLUTION THAT CONTAINED 100 MM SODIUM CACODYLATE AT PH 6.5, 200 MM ZN(OAC)2 AND 10 % (V/V) 2- ...Details: DROPS WERE PREPARED BY MIXING 2MICROL OF THE PROTEIN SOLUTION WITH 1 MICROL OF THE RESERVOIR SOLUTION THAT CONTAINED 100 MM SODIUM CACODYLATE AT PH 6.5, 200 MM ZN(OAC)2 AND 10 % (V/V) 2-PROPANOL. THE BROWNISH CRYSTALS GREW OVER A PERIOD OF 2 MONTHS AT 20 DEGREES C.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.934
DetectorType: ADSC CCD / Detector: CCD / Date: Mar 8, 2002
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.934 Å / Relative weight: 1
ReflectionResolution: 2.6→40 Å / Num. obs: 18702 / % possible obs: 99.2 % / Observed criterion σ(I): 0 / Redundancy: 4.2 % / Rmerge(I) obs: 0.06 / Net I/σ(I): 10.5
Reflection shellResolution: 2.6→2.69 Å / Redundancy: 4.2 % / Rmerge(I) obs: 0.44 / Mean I/σ(I) obs: 2.3 / % possible all: 99.9

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Processing

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

1b2v


Resolution: 2.7→40 Å / Cor.coef. Fo:Fc: 0.936 / Cor.coef. Fo:Fc free: 0.906 / SU B: 9.924 / SU ML: 0.179 / Cross valid method: THROUGHOUT / ESU R: 0.384 / ESU R Free: 0.288 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.274 494 4.8 %RANDOM
Rwork0.236 ---
obs0.238 9813 99.2 %-
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: 41.22 Å2
Baniso -1Baniso -2Baniso -3
1-4.25 Å22.12 Å20 Å2
2--4.25 Å20 Å2
3----6.37 Å2
Refinement stepCycle: LAST / Resolution: 2.7→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1260 0 59 68 1387
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0140.0211393
X-RAY DIFFRACTIONr_bond_other_d0.0020.021122
X-RAY DIFFRACTIONr_angle_refined_deg1.5332.1231925
X-RAY DIFFRACTIONr_angle_other_deg0.9332593
X-RAY DIFFRACTIONr_dihedral_angle_1_deg8.685173
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_restr0.0870.2194
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021631
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02268
X-RAY DIFFRACTIONr_nbd_refined0.2460.2353
X-RAY DIFFRACTIONr_nbd_other0.2250.21371
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other0.0910.2737
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.2590.252
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.280.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.210.213
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.5571.5853
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.03521339
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.013540
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.5794.5586
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
LS refinement shellResolution: 2.7→2.77 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.354 43
Rwork0.357 721

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