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- PDB-1g3q: CRYSTAL STRUCTURE ANALYSIS OF PYROCOCCUS FURIOSUS CELL DIVISION A... -

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Basic information

Entry
Database: PDB / ID: 1g3q
TitleCRYSTAL STRUCTURE ANALYSIS OF PYROCOCCUS FURIOSUS CELL DIVISION ATPASE MIND
ComponentsCELL DIVISION INHIBITOR
Keywordscell cycle / hydrolase / ALPHA-BETA-ALPHA layered / PROTEIN-ADP COMPLEX
Function / homology
Function and homology information


ATP binding / metal ion binding
Similarity search - Function
ATP binding protein MinD, archaea / ATP binding protein MinD/FleN / : / AAA domain / AAA domain / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Cell division inhibitor minD homolog
Similarity search - Component
Biological speciesPyrococcus furiosus (archaea)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 2 Å
AuthorsHayashi, I. / Oyama, T. / Morikawa, K.
CitationJournal: EMBO J. / Year: 2001
Title: Structural and functional studies of MinD ATPase: implications for the molecular recognition of the bacterial cell division apparatus.
Authors: Hayashi, I. / Oyama, T. / Morikawa, K.
History
DepositionOct 25, 2000Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 21, 2001Provider: repository / Type: Initial release
Revision 1.1Apr 27, 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 / 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_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.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_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: CELL DIVISION INHIBITOR
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,7873
Polymers25,3351
Non-polymers4522
Water2,198122
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)96.040, 96.040, 96.040
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number198
Cell settingcubic
Space group name H-MP213

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Components

#1: Protein CELL DIVISION INHIBITOR / MIND ATPASE


Mass: 25335.346 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: ADP-BOUND FORM / Source: (gene. exp.) Pyrococcus furiosus (archaea) / Gene: MIND / Plasmid: PET28A / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) / References: UniProt: Q8U3I1
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Comment: ADP, energy-carrying molecule*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 122 / 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: 2.91 Å3/Da / Density % sol: 57.76 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: MPD, sodium citrate, MgCl2, pH 5.5. Vapor diffusion, hanging drop at 293K, VAPOR DIFFUSION, HANGING DROP
Crystal
*PLUS
Density % sol: 56 %
Crystal grow
*PLUS
Temperature: 20 ℃
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
18 %MPD1reservoir
20.2 M1reservoirMgCl2
30.1 Msodium citrate1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL41XU / Wavelength: 0.71 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Jun 1, 2000
RadiationMonochromator: double-crystal-monochromator / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.71 Å / Relative weight: 1
ReflectionResolution: 2→27.7 Å / Num. obs: 20215 / % possible obs: 100 % / Observed criterion σ(F): 1 / Redundancy: 11 % / Biso Wilson estimate: 11.2 Å2 / Rmerge(I) obs: 0.078 / Net I/σ(I): 4.5
Reflection shellResolution: 2→2.11 Å / Redundancy: 11.1 % / Rmerge(I) obs: 0.24 / % possible all: 99.9
Reflection
*PLUS
Lowest resolution: 39.2 Å
Reflection shell
*PLUS
% possible obs: 100 %

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Processing

Software
NameVersionClassification
SHARPphasing
CNS0.9refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MIR / Resolution: 2→19.61 Å / Rfactor Rfree error: 0.008 / Data cutoff high absF: 2430737.92 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.236 981 4.9 %RANDOM
Rwork0.213 ---
obs0.213 20176 99.8 %-
all-21158 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 42.19 Å2 / ksol: 0.343 e/Å3
Displacement parametersBiso mean: 22.4 Å2
Baniso -1Baniso -2Baniso -3
1-0 Å20 Å20 Å2
2--0 Å20 Å2
3---0 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.27 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.12 Å0.07 Å
Refinement stepCycle: LAST / Resolution: 2→19.61 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1774 0 28 122 1924
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.005
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d22.3
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.84
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it0.61.5
X-RAY DIFFRACTIONc_mcangle_it1.032
X-RAY DIFFRACTIONc_scbond_it0.92
X-RAY DIFFRACTIONc_scangle_it1.422.5
LS refinement shellResolution: 2→2.04 Å / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.2574 56 5 %
Rwork0.2092 3124 -
obs-1022 -
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PAPROTEIN.TOP
X-RAY DIFFRACTION2WATER.PARAMWATER.TOP
X-RAY DIFFRACTION3ADP_XPLOR.PARADP_XPLOR.TOP
X-RAY DIFFRACTION4MG_XPLOR.PMG_XPLOR.TOP
Software
*PLUS
Name: CNS / Version: 0.9 / Classification: refinement
Refinement
*PLUS
Lowest resolution: 19.6 Å / Num. reflection all: 19195
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.3
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.84

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