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- PDB-4czg: C. crescentus MreB, single filament, ADP, A22 inhibitor -

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Basic information

Entry
Database: PDB / ID: 4czg
TitleC. crescentus MreB, single filament, ADP, A22 inhibitor
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
ADENOSINE-5'-DIPHOSPHATE / 3,4-dichlorobenzyl carbamimidothioate / Cell shape-determining protein MreB / Cell shape-determining protein MreB
Similarity search - Component
Biological speciesCAULOBACTER VIBRIOIDES (bacteria)
MethodX-RAY DIFFRACTION / MOLECULAR REPLACEMENT / Resolution: 1.5 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 ...Atomic model / Database references / Derived calculations / 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_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_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

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Assembly

Deposited unit
A: ROD SHAPE-DETERMINING PROTEIN MREB
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,5524
Polymers36,8651
Non-polymers6873
Water7,819434
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)50.674, 73.678, 54.233
Angle α, β, γ (deg.)90.00, 102.39, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein ROD SHAPE-DETERMINING PROTEIN MREB


Mass: 36865.496 Da / Num. of mol.: 1 / Fragment: RESIDUES 9-347 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: M-I9-CCMREB(F102S, V103G)-A347-GSHHHHHH / 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-QH3 / 3,4-dichlorobenzyl carbamimidothioate / A22 (antibiotic)


Mass: 235.134 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H8Cl2N2S / Comment: antibiotic*YM
#3: Chemical ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE / Adenosine diphosphate


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


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 434 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsA22, S-(3,4-DICHLOROBENZYL)ISOTHIOUREA HYDROCHLORIDE (A2S): SML0471 SIGMA

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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: 2.68 Å3/Da / Density % sol: 54.14 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-E / Wavelength: 1.5418
DetectorType: MARESEARCH / Detector: IMAGE PLATE
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 1.5→50 Å / Num. obs: 52173 / % possible obs: 87.8 % / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 20.8 Å2 / Rmerge(I) obs: 0.05 / Net I/σ(I): 19.8
Reflection shellResolution: 1.5→1.58 Å / Redundancy: 5.4 % / Rmerge(I) obs: 0.69 / Mean I/σ(I) obs: 1.1 / % possible all: 77

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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: 1.5→20.397 Å / SU ML: 0.45 / σ(F): 1.34 / Phase error: 23.25 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2177 5297 5 %
Rwork0.1638 --
obs0.1666 106001 86.42 %
Solvent computationShrinkage radii: 0.77 Å / VDW probe radii: 0.9 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 60.873 Å2 / ksol: 0.459 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--3.5757 Å20 Å20.6529 Å2
2--2.5786 Å20 Å2
3---0.9971 Å2
Refinement stepCycle: LAST / Resolution: 1.5→20.397 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2370 0 41 434 2845
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0122439
X-RAY DIFFRACTIONf_angle_d1.3853300
X-RAY DIFFRACTIONf_dihedral_angle_d15.002924
X-RAY DIFFRACTIONf_chiral_restr0.073389
X-RAY DIFFRACTIONf_plane_restr0.006428
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.5-1.5170.3221450.28072756X-RAY DIFFRACTION71
1.517-1.53490.34691460.27252831X-RAY DIFFRACTION72
1.5349-1.55360.32511550.24342924X-RAY DIFFRACTION76
1.5536-1.57330.28261460.22613039X-RAY DIFFRACTION77
1.5733-1.59390.29041600.21993063X-RAY DIFFRACTION79
1.5939-1.61580.3441480.19863071X-RAY DIFFRACTION80
1.6158-1.63880.23561700.19083228X-RAY DIFFRACTION81
1.6388-1.66330.26851710.19313157X-RAY DIFFRACTION84
1.6633-1.68930.27422000.17983300X-RAY DIFFRACTION84
1.6893-1.7170.27681850.17373218X-RAY DIFFRACTION86
1.717-1.74650.26211930.16953351X-RAY DIFFRACTION85
1.7465-1.77830.26531560.16873376X-RAY DIFFRACTION88
1.7783-1.81250.25271600.17433420X-RAY DIFFRACTION87
1.8125-1.84940.24661870.19873407X-RAY DIFFRACTION89
1.8494-1.88960.37711530.23523164X-RAY DIFFRACTION81
1.8896-1.93360.28841720.20723462X-RAY DIFFRACTION88
1.9336-1.98190.23391550.16953502X-RAY DIFFRACTION90
1.9819-2.03540.19022090.14323553X-RAY DIFFRACTION91
2.0354-2.09520.18911920.14843593X-RAY DIFFRACTION92
2.0952-2.16280.18062000.1533573X-RAY DIFFRACTION93
2.1628-2.240.22641440.16643559X-RAY DIFFRACTION91
2.24-2.32960.26722070.16243489X-RAY DIFFRACTION91
2.3296-2.43540.20952070.13733674X-RAY DIFFRACTION94
2.4354-2.56360.19261610.143721X-RAY DIFFRACTION95
2.5636-2.72390.18442120.13953699X-RAY DIFFRACTION96
2.7239-2.93360.18162040.13553719X-RAY DIFFRACTION96
2.9336-3.22780.19042030.14073735X-RAY DIFFRACTION96
3.2278-3.69250.20162120.16093666X-RAY DIFFRACTION95
3.6925-4.64310.19621880.15133450X-RAY DIFFRACTION89
4.6431-20.39870.21461560.20013004X-RAY DIFFRACTION77

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