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- PDB-4czj: C. crescentus MreB, double filament, AMPPNP -

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Basic information

Entry
Database: PDB / ID: 4czj
TitleC. crescentus MreB, double filament, AMPPNP
ComponentsROD SHAPE-DETERMINING PROTEIN MREB
KeywordsSTRUCTURAL PROTEIN / BACTERIAL ACTIN / BACTERIAL CYTOSKELETON
Function / homology
Function and homology information


cell morphogenesis / regulation of cell shape / ATP binding / cytoplasm
Similarity search - Function
Cell shape determining protein MreB / : / MreB/Mbl protein / ATPase, substrate binding domain, subdomain 4 / Actin; Chain A, domain 4 / ATPase, nucleotide binding domain / ATPase, nucleotide binding domain / Nucleotidyltransferase; domain 5 / Alpha-Beta Complex / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER / Cell shape-determining protein MreB / Cell shape-determining protein MreB
Similarity search - Component
Biological speciesCAULOBACTER VIBRIOIDES (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsLowe, J. / van den Ent, F.
CitationJournal: Elife / Year: 2014
Title: Bacterial Actin Mreb Forms Antiparallel Double Filaments.
Authors: Van Den Ent, F. / Izore, T. / Bharat, T.A. / Johnson, C.M. / Lowe, J.
History
DepositionApr 19, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 11, 2014Provider: repository / Type: Initial release
Revision 1.1Jun 25, 2014Group: Atomic model / Database references / Other
Revision 1.2Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / 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.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.value / _struct_conn.pdbx_dist_value / _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_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: ROD SHAPE-DETERMINING PROTEIN MREB
B: ROD SHAPE-DETERMINING PROTEIN MREB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,7926
Polymers73,7312
Non-polymers1,0614
Water5,747319
1
A: ROD SHAPE-DETERMINING PROTEIN MREB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3963
Polymers36,8651
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: ROD SHAPE-DETERMINING PROTEIN MREB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,3963
Polymers36,8651
Non-polymers5312
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)51.497, 101.931, 122.697
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 ROD SHAPE-DETERMINING PROTEIN MREB / MREB


Mass: 36865.496 Da / Num. of mol.: 2 / Fragment: RESIDUES 9-347 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) CAULOBACTER VIBRIOIDES (bacteria) / Plasmid: PHIS17 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3) / Variant (production host): C41 / References: UniProt: B8H609, UniProt: A0A0H3C7V4*PLUS
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-ANP / PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER


Mass: 506.196 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H17N6O12P3 / Comment: AMP-PNP, energy-carrying molecule analogue*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 319 / 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: 2.18 Å3/Da / Density % sol: 43.68 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 0.97938
DetectorType: DECTRIS PILATUS / Detector: PIXEL
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97938 Å / Relative weight: 1
ReflectionResolution: 2→50 Å / Num. obs: 42937 / % possible obs: 97.1 % / Observed criterion σ(I): 0 / Redundancy: 5.2 % / Biso Wilson estimate: 22.78 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 11.3
Reflection shellResolution: 2→2.11 Å / Redundancy: 5.2 % / Rmerge(I) obs: 0.55 / Mean I/σ(I) obs: 3 / % possible all: 98.4

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Processing

Software
NameVersionClassification
PHENIX(PHENIX.REFINE)refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1JCE

1jce


Resolution: 2→47.067 Å / SU ML: 0.47 / σ(F): 1.23 / Phase error: 21.68 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2276 3927 5 %
Rwork0.1758 --
obs0.1784 42937 93.96 %
Solvent computationShrinkage radii: 0.6 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 52.284 Å2 / ksol: 0.382 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--4.8271 Å20 Å2-0 Å2
2--6.9748 Å2-0 Å2
3----2.1477 Å2
Refinement stepCycle: LAST / Resolution: 2→47.067 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4647 0 64 319 5030
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0124766
X-RAY DIFFRACTIONf_angle_d1.3866456
X-RAY DIFFRACTIONf_dihedral_angle_d13.8861784
X-RAY DIFFRACTIONf_chiral_restr0.075770
X-RAY DIFFRACTIONf_plane_restr0.006835
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.02440.31931290.24992691X-RAY DIFFRACTION96
2.0244-2.050.28241450.23682778X-RAY DIFFRACTION95
2.05-2.0770.25681410.22982705X-RAY DIFFRACTION95
2.077-2.10550.2851670.21432665X-RAY DIFFRACTION96
2.1055-2.13560.26421560.20952771X-RAY DIFFRACTION96
2.1356-2.16740.26741150.20092748X-RAY DIFFRACTION95
2.1674-2.20130.24581540.19472744X-RAY DIFFRACTION97
2.2013-2.23740.27611370.18572790X-RAY DIFFRACTION96
2.2374-2.2760.23581420.18232693X-RAY DIFFRACTION96
2.276-2.31730.25331430.19432783X-RAY DIFFRACTION96
2.3173-2.36190.25761490.18922714X-RAY DIFFRACTION96
2.3619-2.41010.26171410.17662750X-RAY DIFFRACTION96
2.4101-2.46250.22551390.16652789X-RAY DIFFRACTION96
2.4625-2.51980.23021750.17212647X-RAY DIFFRACTION95
2.5198-2.58280.26011210.16642797X-RAY DIFFRACTION95
2.5828-2.65260.23921150.17082693X-RAY DIFFRACTION95
2.6526-2.73070.25141110.16872758X-RAY DIFFRACTION95
2.7307-2.81880.25041650.16612657X-RAY DIFFRACTION94
2.8188-2.91960.23341480.16632695X-RAY DIFFRACTION94
2.9196-3.03640.20771290.16642700X-RAY DIFFRACTION94
3.0364-3.17460.23251380.16692647X-RAY DIFFRACTION93
3.1746-3.34190.23721190.15662667X-RAY DIFFRACTION93
3.3419-3.55120.19871390.15742608X-RAY DIFFRACTION92
3.5512-3.82530.20471190.15922650X-RAY DIFFRACTION92
3.8253-4.21010.1921650.1542559X-RAY DIFFRACTION90
4.2101-4.81870.17071450.14132544X-RAY DIFFRACTION89
4.8187-6.06910.21221350.1922539X-RAY DIFFRACTION89
6.0691-47.07960.2321450.20422485X-RAY DIFFRACTION87

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