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- PDB-1n0g: Crystal Structure of A Cell Division and Cell Wall Biosynthesis P... -

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Basic information

Entry
Database: PDB / ID: 1n0g
TitleCrystal Structure of A Cell Division and Cell Wall Biosynthesis Protein UPF0040 from Mycoplasma pneumoniae: Indication of A Novel Fold with A Possible New Conserved Sequence Motif
ComponentsProtein mraZ
KeywordsBIOSYNTHETIC PROTEIN / Cell Division / cell wall biosynthesis protein / Structural Genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center
Function / homology
Function and homology information


negative regulation of DNA-templated transcription initiation / nucleoid / transcription cis-regulatory region binding / DNA-binding transcription factor activity / cytoplasm
Similarity search - Function
Transcriptional regulator MraZ domain / Transcriptional regulator MraZ / MraZ domain / MraZ, C-terminal / MraZ superfamily / MraZ protein, putative antitoxin-like / Chemotaxis protein chec / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / SpoVT-AbrB domain superfamily ...Transcriptional regulator MraZ domain / Transcriptional regulator MraZ / MraZ domain / MraZ, C-terminal / MraZ superfamily / MraZ protein, putative antitoxin-like / Chemotaxis protein chec / SpoVT-AbrB domain profile. / SpoVT-AbrB domain / SpoVT-AbrB domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Transcriptional regulator MraZ
Similarity search - Component
Biological speciesMycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.8 Å
AuthorsChen, S. / Jancarik, J. / Yokota, H. / Kim, R. / Kim, S.-H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Proteins / Year: 2004
Title: Crystal structure of a protein associated with cell division from Mycoplasma pneumoniae (GI: 13508053): a novel fold with a conserved sequence motif.
Authors: Chen, S. / Jancrick, J. / Yokota, H. / Kim, R. / Kim, S.-H.
History
DepositionOct 13, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 16, 2011Group: Atomic model
Revision 1.4Feb 14, 2024Group: Data collection / Database references
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Protein mraZ
B: Protein mraZ


Theoretical massNumber of molelcules
Total (without water)38,6862
Polymers38,6862
Non-polymers00
Water1,38777
1
A: Protein mraZ
B: Protein mraZ

A: Protein mraZ
B: Protein mraZ

A: Protein mraZ
B: Protein mraZ

A: Protein mraZ
B: Protein mraZ


Theoretical massNumber of molelcules
Total (without water)154,7438
Polymers154,7438
Non-polymers00
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
crystal symmetry operation3_665-y+1,x+1,z1
crystal symmetry operation4_465y-1,-x+1,z1
Buried area23500 Å2
ΔGint-149 kcal/mol
Surface area45700 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)101.442, 101.442, 38.193
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number75
Space group name H-MP4
Components on special symmetry positions
IDModelComponents
11A-183-

HOH

DetailsThe biological assembly is an octamer ring structure.

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Components

#1: Protein Protein mraZ / UPF0040 Pfam protein


Mass: 19342.865 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mycoplasma pneumoniae (Filterable agent of primary atypical pneumonia)
Production host: Escherichia coli (E. coli) / References: UniProt: P75467
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / 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: 51.56 %
Crystal growMethod: vapor diffusion, hanging drop / Details: VAPOR DIFFUSION, HANGING DROP
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 8.5 / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formulaDetails
119 mg/mlprotein1drop
20.5 M1dropNaCl
30.2 M1dropLi2SO4
40.1 MTris-HCl1droppH8.5
518 %(w/v)PEG33501drop
620 %glycerol1drop

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Oct 17, 2001
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.8→38.19 Å / Num. all: 9903 / Num. obs: 9888 / % possible obs: 99 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 0 / Redundancy: 6.8 % / Biso Wilson estimate: 104.4 Å2 / Rsym value: 0.046 / Net I/σ(I): 22.4
Reflection shellResolution: 2.8→2.85 Å / Redundancy: 6.7 % / Mean I/σ(I) obs: 3.5 / Rsym value: 0.285 / % possible all: 100
Reflection
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / % possible obs: 99.9 % / Rmerge(I) obs: 0.046
Reflection shell
*PLUS
% possible obs: 100 % / Num. unique obs: 486 / Rmerge(I) obs: 0.285

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Processing

Software
NameVersionClassification
HKL-2000data collection
SCALEPACKdata scaling
AMoREphasing
CNS1refinement
HKL-2000data reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.8→29.22 Å / Rfactor Rfree error: 0.013 / Data cutoff high absF: 2042801.6 / Data cutoff high rms absF: 2042801.6 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 2 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.283 475 4.8 %RANDOM
Rwork0.229 ---
all-9888 --
obs-9819 99.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 35.7846 Å2 / ksol: 0.333832 e/Å3
Displacement parametersBiso mean: 48 Å2
Baniso -1Baniso -2Baniso -3
1--2.41 Å20 Å20 Å2
2---2.41 Å20 Å2
3---4.82 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.46 Å0.36 Å
Luzzati d res low-5 Å
Luzzati sigma a0.49 Å0.41 Å
Refinement stepCycle: LAST / Resolution: 2.8→29.22 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2306 0 0 77 2383
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_angle_deg1.5
X-RAY DIFFRACTIONc_dihedral_angle_d22.9
X-RAY DIFFRACTIONc_improper_angle_d0.77
X-RAY DIFFRACTIONc_mcbond_it1.291.5
X-RAY DIFFRACTIONc_mcangle_it2.242
X-RAY DIFFRACTIONc_scbond_it1.632
X-RAY DIFFRACTIONc_scangle_it2.692.5
Refine LS restraints NCSNCS model details: CONSTR
LS refinement shellResolution: 2.8→2.98 Å / Rfactor Rfree error: 0.036 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.335 88 5.5 %
Rwork0.32 1503 -
obs--98.2 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMWATER.TOP
Refinement
*PLUS
Highest resolution: 2.8 Å / Lowest resolution: 20 Å / Rfactor Rfree: 0.278 / Rfactor Rwork: 0.228
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg22.9
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.78

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