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- PDB-4g7w: Crystal structure of the N-terminal domain of the minor coat prot... -

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Basic information

Entry
Database: PDB / ID: 4g7w
TitleCrystal structure of the N-terminal domain of the minor coat protein pIII from CTXphi
ComponentsPutative uncharacterized protein
KeywordsPROTEIN BINDING / beta barrel / TolA binding domain / selenomethionine-substituted protein / phage coat
Function / homologyVibrio phage CTXphi pIII, N-terminal N1 domain / Elongation Factor Tu (Ef-tu); domain 3 / Beta Barrel / Mainly Beta / :
Function and homology information
Biological speciesVibrio cholerae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.9 Å
AuthorsKolappan, S. / Ford, C.G. / Craig, L.
CitationJournal: J.Biol.Chem. / Year: 2012
Title: Crystal Structures of a CTX{varphi} pIII Domain Unbound and in Complex with a Vibrio cholerae TolA Domain Reveal Novel Interaction Interfaces.
Authors: Ford, C.G. / Kolappan, S. / Phan, H.T. / Waldor, M.K. / Winther-Larsen, H.C. / Craig, L.
History
DepositionJul 20, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 29, 2012Provider: repository / Type: Initial release
Revision 1.1Sep 19, 2012Group: Database references
Revision 1.2Nov 7, 2012Group: Database references
Revision 1.3Nov 20, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_special_symmetry / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Putative uncharacterized protein
B: Putative uncharacterized protein
C: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)52,8833
Polymers52,8833
Non-polymers00
Water1629
1
A: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)17,6281
Polymers17,6281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)17,6281
Polymers17,6281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative uncharacterized protein


Theoretical massNumber of molelcules
Total (without water)17,6281
Polymers17,6281
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)126.250, 126.250, 128.270
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322
Components on special symmetry positions
IDModelComponents
11C-202-

HOH

Noncrystallographic symmetry (NCS)NCS oper:
IDCodeMatrixVector
1given(1), (1), (1)
2given(-0.957847, -0.016824, -0.286787), (-0.030308, -0.986795, 0.159116), (-0.285677, 0.161101, 0.944688)80.96861, 140.42337, 0.02828
3given(0.56346, 0.79887, 0.210523), (-0.300275, 0.435436, -0.848664), (-0.769641, 0.414973, 0.485232)-17.33102, 85.57391, -7.76148

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Components

#1: Protein Putative uncharacterized protein


Mass: 17627.809 Da / Num. of mol.: 3 / Fragment: N-terminal domain
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio cholerae (bacteria) / Strain: CIRS101 / Gene: orfU, VCH_002198 / Production host: Escherichia coli (E. coli) / References: UniProt: C6RZG1
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 9 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY

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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: 2.79 Å3/Da / Density % sol: 55.92 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 20 mM Bis Tris, 50 mM NaCl, Fos-Choline-9, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-2 / Wavelength: 0.91837, 0.97922
DetectorType: MARMOSAIC 325 mm CCD / Detector: CCD / Date: Dec 13, 2011 / Details: mirrors
RadiationMonochromator: Double crystal monochromator, Si(111) / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918371
20.979221
ReflectionResolution: 2.9→20 Å / Num. obs: 13171 / % possible obs: 99.6 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2.14
Reflection shell
Resolution (Å)Diffraction-ID% possible all
2.9-2.98199.9
2.98-3.06199.9
3.06-3.151100
3.15-3.241100
3.24-3.241100
3.35-3.471100

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Processing

Software
NameVersionClassification
Blu-Icedata collection
SOLVEphasing
REFMAC5.6.0117refinement
XDSdata reduction
XSCALEdata scaling
RefinementMethod to determine structure: MAD / Resolution: 2.9→19.99 Å / Cor.coef. Fo:Fc: 0.922 / Cor.coef. Fo:Fc free: 0.907 / SU B: 31.984 / SU ML: 0.275 / Cross valid method: THROUGHOUT / ESU R: 0.503 / ESU R Free: 0.32 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.26193 694 5 %RANDOM
Rwork0.232 ---
all0.234 ---
obs0.234 13171 99.53 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 78.454 Å2
Baniso -1Baniso -2Baniso -3
1-3.59 Å21.8 Å20 Å2
2--3.59 Å20 Å2
3----5.39 Å2
Refinement stepCycle: LAST / Resolution: 2.9→19.99 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2229 0 0 9 2238
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.022318
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.8531.9683166
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4365294
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.68425100
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.86615315
X-RAY DIFFRACTIONr_dihedral_angle_4_deg14.96156
X-RAY DIFFRACTIONr_chiral_restr0.1180.2327
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0221820
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.974 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.349 45 -
Rwork0.342 803 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.942-0.50620.79332.74070.2525.03780.0185-0.59910.75890.19320.16730.0601-0.5622-0.0898-0.18580.4093-0.04870.16110.4788-0.19780.413136.780783.325613.7745
21.65060.35070.19252.7725-0.16776.16650.2406-0.1431-0.1304-0.0745-0.0657-0.71530.19690.939-0.17490.13790.08530.02360.4309-0.05330.305640.398659.079916.7161
310.9870.3732-0.70710.4216-0.99972.6725-0.32970.6986-0.6442-0.37930.29570.09080.7764-0.84190.03390.4773-0.0908-0.14550.4064-0.08440.28714.256150.961423.3985
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 98
2X-RAY DIFFRACTION2B2 - 99
3X-RAY DIFFRACTION3C1 - 99

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