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- PDB-2onr: Crystal structure of A. fulgidus periplasmic binding protein ModA... -

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Basic information

Entry
Database: PDB / ID: 2onr
TitleCrystal structure of A. fulgidus periplasmic binding protein ModA with bound molybdate
ComponentsUPF0100 protein AF_0094
KeywordsLIGAND BINDING PROTEIN / soluble protein
Function / homology
Function and homology information


tungstate binding / metal ion binding / plasma membrane
Similarity search - Function
Tungstate ABC transporter, substrate-binding protein WtpA / Bacterial extracellular solute-binding protein / Bacterial extracellular solute-binding protein / Periplasmic binding protein-like II / D-Maltodextrin-Binding Protein; domain 2 / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
MOLYBDATE ION / NITRATE ION / Molybdate/tungstate-binding protein WtpA
Similarity search - Component
Biological speciesArchaeoglobus fulgidus DSM 4304 (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.6 Å
AuthorsHollenstein, K. / Frei, D.C. / Locher, K.P.
CitationJournal: Nature / Year: 2007
Title: Structure of an ABC transporter in complex with its binding protein.
Authors: Hollenstein, K. / Frei, D.C. / Locher, K.P.
History
DepositionJan 24, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Mar 6, 2007Provider: repository / Type: Initial release
Revision 1.1May 1, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Dec 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_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_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_comp_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_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_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_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_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: UPF0100 protein AF_0094
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,0886
Polymers35,7181
Non-polymers3705
Water5,008278
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)75.845, 75.845, 115.000
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein UPF0100 protein AF_0094


Mass: 35717.785 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Archaeoglobus fulgidus DSM 4304 (archaea)
Species: Archaeoglobus fulgidus / Strain: VC-16, DSM 4304, JCM 9628, NBRC 100126 / Gene: AF_0094 / Production host: Escherichia coli (E. coli) / References: UniProt: O30142
#2: Chemical ChemComp-NO3 / NITRATE ION / Nitrate


Mass: 62.005 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: NO3
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-MOO / MOLYBDATE ION / MOLYBDATE / Molybdate


Mass: 159.938 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: MoO4
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 278 / 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: 2.31 Å3/Da / Density % sol: 46.85 %

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Data collection

Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06SA
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthRelative weight: 1
ReflectionResolution: 1.6→19.76 Å / Num. obs: 44754

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Processing

Software
NameVersionClassificationNB
CNSrefinement
PDB_EXTRACT2data extraction
HKL-2000data reduction
HKL-2000data scaling
ARP/wARPmodel building
RefinementMethod to determine structure: SAD / Resolution: 1.6→19.76 Å
RfactorNum. reflection% reflection
Rfree0.235 --
Rwork0.178 --
obs0.178 44754 99.5 %
Displacement parametersBiso mean: 23 Å2
Refinement stepCycle: LAST / Resolution: 1.6→19.76 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2548 0 18 278 2844
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.0124
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.58
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it
X-RAY DIFFRACTIONc_mcangle_it
X-RAY DIFFRACTIONc_scbond_it
X-RAY DIFFRACTIONc_scangle_it

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