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- PDB-1atg: AZOTOBACTER VINELANDII PERIPLASMIC MOLYBDATE-BINDING PROTEIN -

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Basic information

Entry
Database: PDB / ID: 1atg
TitleAZOTOBACTER VINELANDII PERIPLASMIC MOLYBDATE-BINDING PROTEIN
ComponentsPERIPLASMIC MOLYBDATE-BINDING PROTEIN
KeywordsBINDING PROTEIN / MOLYBDATE / TUNGSTATE / PERIPLASM / ABC TRANSPORTER
Function / homology
Function and homology information


molybdate ion binding / molybdate ion transport / metal ion binding
Similarity search - Function
AvModA-like, substrate binding domain / Molybdate ABC transporter, substrate-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
ACETATE ION / TUNGSTATE(VI)ION / Binding protein
Similarity search - Component
Biological speciesAzotobacter vinelandii (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SINGLE ISOMORPHOUS REPLACEMENT WITH ANOMALOUS SCATTERING / Resolution: 1.2 Å
AuthorsLawson, D.M. / Pau, R.N. / Williams, C.E.M. / Mitchenall, L.A.
Citation
Journal: Structure / Year: 1998
Title: Ligand size is a major determinant of specificity in periplasmic oxyanion-binding proteins: the 1.2 A resolution crystal structure of Azotobacter vinelandii ModA.
Authors: Lawson, D.M. / Williams, C.E. / Mitchenall, L.A. / Pau, R.N.
#1: Journal: J.Chem.Soc.,Dalton Trans. / Year: 1997
Title: Protein Ligands for Molybdate. Specificity and Charge Stabilisation at the Anion-Binding Sites of Periplasmic and Intracellular Molybdate-Binding Proteins of Azotobacter Vinelandii
Authors: Lawson, D.M. / Williams, C.E.M. / White, D.J. / Choay, A.P. / Mitchenall, L.A. / Pau, R.N.
History
DepositionAug 14, 1997Processing site: BNL
Revision 1.0Oct 14, 1998Provider: repository / Type: Initial release
Revision 1.1Mar 3, 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 / diffrn_source / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _diffrn_source.pdbx_synchrotron_site / _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
A: PERIPLASMIC MOLYBDATE-BINDING PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)24,9186
Polymers24,3911
Non-polymers5275
Water6,395355
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)32.934, 88.802, 41.746
Angle α, β, γ (deg.)90.00, 93.55, 90.00
Int Tables number4
Space group name H-MP1211

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Components

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Protein , 1 types, 1 molecules A

#1: Protein PERIPLASMIC MOLYBDATE-BINDING PROTEIN / MODA


Mass: 24390.729 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Azotobacter vinelandii (bacteria) / Cellular location: PERIPLASM / Strain: RP2 / References: UniProt: Q7SIH2

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Non-polymers , 5 types, 360 molecules

#2: Chemical ChemComp-WO4 / TUNGSTATE(VI)ION


Mass: 247.838 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: WO4
#3: Chemical ChemComp-ACT / ACETATE ION / Acetate


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL / Ethylene glycol


Mass: 62.068 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C2H6O2
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 355 / 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: 2.54 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 4
Details: HANGING DROP VAPOUR DIFFUSION WITH PROTEIN CONCENTRATION IN THE RANGE 10-15 MG/ML IN 10MM TRIS-HCL PH 7.0. 1 OR 2 MICROLITER DROPS OF THE LATTER WERE MIXED WITH AN EQUAL VOLUME OF 11-14% ...Details: HANGING DROP VAPOUR DIFFUSION WITH PROTEIN CONCENTRATION IN THE RANGE 10-15 MG/ML IN 10MM TRIS-HCL PH 7.0. 1 OR 2 MICROLITER DROPS OF THE LATTER WERE MIXED WITH AN EQUAL VOLUME OF 11-14% (W/V) PEG 4000 AND 0.4M AMMONIUM SULFATE IN 0.1M ACETATE BUFFER AT PH 4.0, AND THEN EQUILIBRATED AGAINST THIS SOLUTION AT 18 DEG C. CRYOPROTECTED USING THE SAME SOLUTION CONTAINING 25% (V/V) ETHYLENE GLYCOL., vapor diffusion - hanging drop, temperature 291K
PH range: 4.0-7.0
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 18 ℃ / pH: 7 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110-15 mg/mlprotein1drop
210 mMTris-HCl1drop
31 mMsodium molybdate1dropcan be replaced by 1mM sodium tungstate
411-14 %(w/v)PEG40001reservoir
50.4 Mammonium sulfate1reservoir
60.1 Msodium acetate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: EMBL/DESY, HAMBURG / Beamline: X11 / Wavelength: 0.9116
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Sep 1, 1996 / Details: MIRRORS
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9116 Å / Relative weight: 1
ReflectionResolution: 1.2→100 Å / Num. obs: 74061 / % possible obs: 99.4 % / Observed criterion σ(I): 0 / Redundancy: 3.7 % / Rmerge(I) obs: 0.094 / Net I/σ(I): 12.7
Reflection shellResolution: 1.2→1.22 Å / Redundancy: 3.2 % / Rmerge(I) obs: 0.161 / Mean I/σ(I) obs: 6.9 / % possible all: 99.1

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Processing

Software
NameVersionClassification
VARIOUSCCP4 PROGRAMS (INCLUDING MLPHAREmodel building
DMmodel building
Omodel building
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4(MLPHAREphasing
DMphasing
OTHERS)phasing
RefinementMethod to determine structure: SINGLE ISOMORPHOUS REPLACEMENT WITH ANOMALOUS SCATTERING
Resolution: 1.2→40 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: LUZZATI ESD BASED ON TEST REFLECTIONS ONLY. PLANE RESTRAINT RMS BASED ON NON-AROMATIC PLANAR GROUPS ONLY.
RfactorNum. reflection% reflectionSelection details
Rfree0.183 3730 5 %RANDOM
Rwork0.1644 ---
obs-74061 99.4 %-
Refine analyzeLuzzati coordinate error obs: 0.13 Å / Luzzati d res low obs: 5 Å
Refinement stepCycle: LAST / Resolution: 1.2→40 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1721 0 22 355 2098
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0070.02
X-RAY DIFFRACTIONp_angle_d0.020.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0260.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.1642
X-RAY DIFFRACTIONp_mcangle_it1.6272.5
X-RAY DIFFRACTIONp_scbond_it2.3043
X-RAY DIFFRACTIONp_scangle_it3.1714.5
X-RAY DIFFRACTIONp_plane_restr0.2250.03
X-RAY DIFFRACTIONp_chiral_restr0.080.15
X-RAY DIFFRACTIONp_singtor_nbd0.1650.3
X-RAY DIFFRACTIONp_multtor_nbd0.2460.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1480.3
X-RAY DIFFRACTIONp_planar_tor47
X-RAY DIFFRACTIONp_staggered_tor13.815
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor23.720
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.164 / Rfactor Rfree: 0.18354 / Rfactor Rwork: 0.1644
Solvent computation
*PLUS
Displacement parameters
*PLUS

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