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- PDB-4m1x: Tetrameric ring structure of 201phi2-1p060 from Pseudomonas phage... -

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Basic information

Entry
Database: PDB / ID: 4m1x
TitleTetrameric ring structure of 201phi2-1p060 from Pseudomonas phage 201phi2-1
Componentsuncharacterized protein 201phi2-1p060
KeywordsUNKNOWN FUNCTION / tetramer / ring / ferredoxin-like fold
Function / homologyGyrase A; domain 2 - #240 / Gyrase A; domain 2 / 2-Layer Sandwich / Alpha Beta / DI(HYDROXYETHYL)ETHER / Uncharacterized protein
Function and homology information
Biological speciesPseudomonas phage 201phi2-1 (virus)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.3 Å
AuthorsPartridge, J.R. / Zehr, E.A. / Agard, D.A.
CitationJournal: To be Published
Title: Tetrameric ring structure of 201phi2-1p060 from Pseudomonas phage 201phi2-1
Authors: Partridge, J.R. / Zehr, E.A. / Agard, D.A.
History
DepositionAug 4, 2013Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 6, 2014Provider: repository / Type: Initial release
Revision 1.1Feb 28, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_ref_seq_dif / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_ref_seq_dif.details / _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: uncharacterized protein 201phi2-1p060
B: uncharacterized protein 201phi2-1p060
C: uncharacterized protein 201phi2-1p060
D: uncharacterized protein 201phi2-1p060
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,2785
Polymers46,1724
Non-polymers1061
Water7,855436
1
A: uncharacterized protein 201phi2-1p060
D: uncharacterized protein 201phi2-1p060
hetero molecules

A: uncharacterized protein 201phi2-1p060
D: uncharacterized protein 201phi2-1p060
hetero molecules


Theoretical massNumber of molelcules
Total (without water)46,3846
Polymers46,1724
Non-polymers2122
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area5550 Å2
ΔGint-28 kcal/mol
Surface area14310 Å2
MethodPISA
2
B: uncharacterized protein 201phi2-1p060
C: uncharacterized protein 201phi2-1p060

B: uncharacterized protein 201phi2-1p060
C: uncharacterized protein 201phi2-1p060


Theoretical massNumber of molelcules
Total (without water)46,1724
Polymers46,1724
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_575-x,-y+2,z1
Buried area5400 Å2
ΔGint-31 kcal/mol
Surface area14020 Å2
MethodPISA
3
A: uncharacterized protein 201phi2-1p060
D: uncharacterized protein 201phi2-1p060
hetero molecules

A: uncharacterized protein 201phi2-1p060
D: uncharacterized protein 201phi2-1p060
hetero molecules

B: uncharacterized protein 201phi2-1p060
C: uncharacterized protein 201phi2-1p060

B: uncharacterized protein 201phi2-1p060
C: uncharacterized protein 201phi2-1p060


Theoretical massNumber of molelcules
Total (without water)92,55710
Polymers92,3448
Non-polymers2122
Water1448
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
crystal symmetry operation3_547-x+1/2,y-1/2,-z+21
crystal symmetry operation4_567x+1/2,-y+3/2,-z+21
Buried area13840 Å2
ΔGint-81 kcal/mol
Surface area25430 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.098, 52.672, 62.302
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-178-

HOH

21C-123-

HOH

31C-135-

HOH

41C-189-

HOH

51C-219-

HOH

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Components

#1: Protein
uncharacterized protein 201phi2-1p060


Mass: 11543.043 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Pseudomonas phage 201phi2-1 (virus) / Plasmid: pET-28a / Production host: Escherichia coli (E. coli) / Strain (production host): BL21-RIL / References: UniProt: B3FK35
#2: Chemical ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H10O3
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 436 / 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: 1.57 Å3/Da / Density % sol: 21.42 %
Crystal growTemperature: 296 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 0.1M Tris pH 8.5, 0.3M NaCl, and 25% PEG3350 , VAPOR DIFFUSION, HANGING DROP, temperature 296K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 8.3.1 / Wavelength: 1.1158, 1.771203
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Sep 2, 2011
RadiationMonochromator: Double flat crystal, Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.11581
21.7712031
ReflectionResolution: 1.3→45 Å / Num. all: 72101 / Num. obs: 70298 / % possible obs: 97.5 % / Observed criterion σ(F): -3 / Observed criterion σ(I): -3 / Redundancy: 4.9 % / Biso Wilson estimate: 14.66 Å2 / Rsym value: 0.066 / Net I/σ(I): 24.96
Reflection shellResolution: 1.3→1.35 Å / Redundancy: 2.3 % / Mean I/σ(I) obs: 3.92 / Num. unique all: 7060 / Rsym value: 0.203 / % possible all: 80.2

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
PHENIX(phenix.refine: 1.8.2_1309)refinement
HKL-2000data reduction
SCALAdata scaling
RefinementMethod to determine structure: SAD / Resolution: 1.3→29.703 Å / SU ML: 0.1 / σ(F): 1.34 / Phase error: 11.67 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.144 2000 2.85 %random
Rwork0.1189 ---
all0.1196 72164 --
obs0.1196 70223 97.31 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 1.3→29.703 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2423 0 7 436 2866
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0082671
X-RAY DIFFRACTIONf_angle_d1.2883613
X-RAY DIFFRACTIONf_dihedral_angle_d11.877986
X-RAY DIFFRACTIONf_chiral_restr0.084385
X-RAY DIFFRACTIONf_plane_restr0.006450
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2988-1.33130.19261100.16413767X-RAY DIFFRACTION77
1.3313-1.36730.18831300.13484416X-RAY DIFFRACTION89
1.3673-1.40760.14051410.11534820X-RAY DIFFRACTION98
1.4076-1.4530.11561440.09344910X-RAY DIFFRACTION100
1.453-1.50490.12841460.08634976X-RAY DIFFRACTION100
1.5049-1.56520.11931450.08734941X-RAY DIFFRACTION100
1.5652-1.63640.13971460.0925005X-RAY DIFFRACTION100
1.6364-1.72270.13111450.09144947X-RAY DIFFRACTION100
1.7227-1.83060.10611460.09054994X-RAY DIFFRACTION100
1.8306-1.97190.1221470.09534984X-RAY DIFFRACTION100
1.9719-2.17030.12871470.10095023X-RAY DIFFRACTION100
2.1703-2.48420.14661490.11695056X-RAY DIFFRACTION100
2.4842-3.12930.16851490.14335102X-RAY DIFFRACTION100
3.1293-29.71060.15461550.14035282X-RAY DIFFRACTION100

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