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- PDB-3mhx: Crystal Structure of Stenotrophomonas maltophilia FeoA complexed ... -

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Basic information

Entry
Database: PDB / ID: 3mhx
TitleCrystal Structure of Stenotrophomonas maltophilia FeoA complexed with Zinc: A Unique Procaryotic SH3 Domain Protein Possibly Acting as a Bacterial Ferrous Iron Transport Activating Factor
ComponentsPutative ferrous iron transport protein A
KeywordsMETAL TRANSPORT / FeoA / ferrous iron transport / zinc binding / prokaryotic SH3 domain / Stenotrophomonus Maltophilia
Function / homology
Function and homology information


transition metal ion binding
Similarity search - Function
FeoA domain / Ferrous iron transport protein A (FeoA) / Ferrous iron transporter FeoA domain / Ferrous iron transporter, core domain / FeoA / Transcriptional repressor, C-terminal / SH3 type barrels. / Roll / Mainly Beta
Similarity search - Domain/homology
ACETATE ION / Putative ferrous iron transport protein A
Similarity search - Component
Biological speciesStenotrophomonas maltophilia (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.7 Å
AuthorsChou, S.-H. / Su, Y.-C. / Chin, K.-H. / Hung, H.-C. / Shen, G.-H. / Wang, A.H.-J.
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Structure of Stenotrophomonas maltophilia FeoA complexed with zinc: a unique prokaryotic SH3-domain protein that possibly acts as a bacterial ferrous iron-transport activating factor
Authors: Su, Y.-C. / Chin, K.-H. / Hung, H.-C. / Shen, G.-H. / Wang, A.H.-J. / Chou, S.-H.
History
DepositionApr 9, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 23, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Mar 20, 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_ref_seq_dif / 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_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_seq_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 / _struct_ref_seq_dif.details / _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: Putative ferrous iron transport protein A
B: Putative ferrous iron transport protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)19,02912
Polymers18,5312
Non-polymers49810
Water3,225179
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1340 Å2
ΔGint-134 kcal/mol
Surface area9010 Å2
MethodPISA
Unit cell
Length a, b, c (Å)46.015, 54.031, 61.035
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative ferrous iron transport protein A


Mass: 9265.683 Da / Num. of mol.: 2 / Mutation: L43M
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Stenotrophomonas maltophilia (bacteria)
Strain: K279a / Gene: feoA, Smlt2210 / Plasmid: pMCsG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-de3 / References: UniProt: B2FQ63
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 179 / 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: 2.05 Å3/Da / Density % sol: 39.92 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 25% v/v PEG 550 MME, 0.1M MES, 0.01M zinc sulfate pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSRRC / Beamline: BL13B1 / Wavelength: 0.97962 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Apr 26, 2009
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97962 Å / Relative weight: 1
ReflectionResolution: 1.7→30 Å / Num. obs: 17106 / Observed criterion σ(I): 2 / Redundancy: 9.3 %

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Processing

Software
NameClassification
HKL-2000data collection
SOLVEphasing
CNSrefinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: SAD / Resolution: 1.7→25.43 Å
RfactorNum. reflection% reflection
Rfree0.228 2559 9.1 %
Rwork0.191 24876 -
obs-17106 98.8 %
Solvent computationBsol: 30.011 Å2
Displacement parametersBiso max: 28.1 Å2 / Biso mean: 13.214 Å2 / Biso min: 2.26 Å2
Baniso -1Baniso -2Baniso -3
1--2.01 Å20 Å20 Å2
2--1.813 Å20 Å2
3---0.197 Å2
Refinement stepCycle: LAST / Resolution: 1.7→25.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1278 0 13 179 1470
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.004
X-RAY DIFFRACTIONc_angle_d1.171
X-RAY DIFFRACTIONc_mcbond_it1.3021.5
X-RAY DIFFRACTIONc_scbond_it2.0842
X-RAY DIFFRACTIONc_mcangle_it1.7882
X-RAY DIFFRACTIONc_scangle_it2.8112.5
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater.top
X-RAY DIFFRACTION3ion.paramion.top

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