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- PDB-4v02: MinC:MinD cell division protein complex, Aquifex aeolicus -

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Basic information

Entry
Database: PDB / ID: 4v02
TitleMinC:MinD cell division protein complex, Aquifex aeolicus
Components
  • PROBABLE SEPTUM SITE-DETERMINING PROTEIN MINC
  • SITE-DETERMINING PROTEIN
KeywordsCELL CYCLE / BACTERIAL CELL DIVISION / FTSZ / MIN SYSTEM
Function / homology
Function and homology information


regulation of cell septum assembly / negative regulation of cell division / division septum assembly / regulation of cell division / cell morphogenesis / cytoplasmic side of plasma membrane / ATP hydrolysis activity / ATP binding / metal ion binding / cytosol
Similarity search - Function
Septum formation inhibitor MinC, N-terminal / ATP binding protein MinD / Septum formation inhibitor MinC, N-terminal domain / Septum formation inhibitor MinC, C-terminal / Septum formation inhibitor MinC / Septum formation inhibitor MinC, C-terminal domain superfamily / Septum formation inhibitor MinC, C-terminal domain / Pectate Lyase C-like - #70 / CobQ/CobB/MinD/ParA nucleotide binding domain / ATP binding protein MinD/FleN ...Septum formation inhibitor MinC, N-terminal / ATP binding protein MinD / Septum formation inhibitor MinC, N-terminal domain / Septum formation inhibitor MinC, C-terminal / Septum formation inhibitor MinC / Septum formation inhibitor MinC, C-terminal domain superfamily / Septum formation inhibitor MinC, C-terminal domain / Pectate Lyase C-like - #70 / CobQ/CobB/MinD/ParA nucleotide binding domain / ATP binding protein MinD/FleN / Cyclase-associated protein CAP/septum formation inhibitor MinC, C-terminal / CobQ/CobB/MinD/ParA nucleotide binding domain / : / Pectate Lyase C-like / 3 Solenoid / P-loop containing nucleotide triphosphate hydrolases / Rossmann fold / P-loop containing nucleoside triphosphate hydrolase / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
ADENOSINE-5'-TRIPHOSPHATE / Septum site-determining protein MinD / Probable septum site-determining protein MinC
Similarity search - Component
Biological speciesAQUIFEX AEOLICUS (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.7 Å
AuthorsGhosal, D. / Lowe, J.
CitationJournal: Nat.Commun. / Year: 2014
Title: Mincd Cell Division Proteins Form Alternating Copolymeric Cytomotive Filaments.
Authors: Ghosal, D. / Trambaiolo, D. / Amos, L.A. / Lowe, J.
History
DepositionSep 10, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 14, 2015Provider: repository / Type: Initial release
Revision 1.1May 8, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / 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_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: SITE-DETERMINING PROTEIN
B: SITE-DETERMINING PROTEIN
C: PROBABLE SEPTUM SITE-DETERMINING PROTEIN MINC
D: PROBABLE SEPTUM SITE-DETERMINING PROTEIN MINC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)86,6088
Polymers85,5454
Non-polymers1,0634
Water00
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area6200 Å2
ΔGint-20.8 kcal/mol
Surface area37730 Å2
MethodPQS
Unit cell
Length a, b, c (Å)130.618, 130.618, 298.507
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number179
Space group name H-MP6522

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Components

#1: Protein SITE-DETERMINING PROTEIN / MIND


Mass: 28697.398 Da / Num. of mol.: 2
Fragment: C-TERMINAL AMPHIPATHIC HELIX REMOVED, UNP RESDIUES 1-250
Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AQUIFEX AEOLICUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O67033
#2: Protein PROBABLE SEPTUM SITE-DETERMINING PROTEIN MINC / MINC


Mass: 14075.339 Da / Num. of mol.: 2 / Fragment: C-TERMINAL DOMAIN, UNP RESIDUES 82-201
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AQUIFEX AEOLICUS (bacteria) / Production host: ESCHERICHIA COLI (E. coli) / References: UniProt: O67034
#3: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#4: Chemical ChemComp-ATP / ADENOSINE-5'-TRIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Comment: ATP, energy-carrying molecule*YM
Sequence detailsAMPHIPATHIC HELIX REMOVED FROM C-TERMINUS, D40A MITATION

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 4.3 Å3/Da / Density % sol: 71 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.9795
DetectorType: ADSC CCD / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 2.7→50 Å / Num. obs: 42285 / % possible obs: 100 % / Observed criterion σ(I): 0 / Redundancy: 14.3 % / Biso Wilson estimate: 52.22 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 20.6
Reflection shellResolution: 2.7→2.85 Å / Redundancy: 12.9 % / Rmerge(I) obs: 0.63 / Mean I/σ(I) obs: 4.6 / % possible all: 100

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.7→49.171 Å / SU ML: 0.33 / σ(F): 1.4 / Phase error: 23.16 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2357 3870 4.9 %
Rwork0.1883 --
obs0.1907 39102 99.95 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.7→49.171 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5602 0 64 0 5666
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0165732
X-RAY DIFFRACTIONf_angle_d1.637741
X-RAY DIFFRACTIONf_dihedral_angle_d17.3682213
X-RAY DIFFRACTIONf_chiral_restr0.088919
X-RAY DIFFRACTIONf_plane_restr0.007968
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.7-2.7330.35241280.27222673X-RAY DIFFRACTION100
2.733-2.76750.34631310.26042665X-RAY DIFFRACTION100
2.7675-2.8040.3551480.23992621X-RAY DIFFRACTION100
2.804-2.84240.24541390.23212687X-RAY DIFFRACTION100
2.8424-2.8830.26271360.2162664X-RAY DIFFRACTION100
2.883-2.9260.28611080.22312667X-RAY DIFFRACTION100
2.926-2.97170.2811590.23982640X-RAY DIFFRACTION100
2.9717-3.02040.27661240.24432654X-RAY DIFFRACTION100
3.0204-3.07250.31081440.22652645X-RAY DIFFRACTION100
3.0725-3.12840.35281390.23592670X-RAY DIFFRACTION100
3.1284-3.18850.30651570.22782647X-RAY DIFFRACTION100
3.1885-3.25360.29991230.2212673X-RAY DIFFRACTION100
3.2536-3.32430.2771310.20282661X-RAY DIFFRACTION100
3.3243-3.40160.2541320.19962640X-RAY DIFFRACTION100
3.4016-3.48670.21411240.18852673X-RAY DIFFRACTION100
3.4867-3.58090.25311260.18822654X-RAY DIFFRACTION100
3.5809-3.68630.21431330.17452659X-RAY DIFFRACTION100
3.6863-3.80520.26371360.17422674X-RAY DIFFRACTION100
3.8052-3.94110.21531310.18762673X-RAY DIFFRACTION100
3.9411-4.09890.22481560.16692649X-RAY DIFFRACTION100
4.0989-4.28530.19721580.16012618X-RAY DIFFRACTION100
4.2853-4.51110.17771460.14632665X-RAY DIFFRACTION100
4.5111-4.79350.1681600.14312629X-RAY DIFFRACTION100
4.7935-5.16330.16681560.15522633X-RAY DIFFRACTION100
5.1633-5.68220.22061460.1732660X-RAY DIFFRACTION100
5.6822-6.50280.26441130.19152680X-RAY DIFFRACTION100
6.5028-8.18670.25121490.18932638X-RAY DIFFRACTION100
8.1867-49.17890.23151370.1912623X-RAY DIFFRACTION99

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