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- PDB-4ghj: 1.75 Angstrom Crystal Structure of Transcriptional Regulator ftom... -

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Basic information

Entry
Database: PDB / ID: 4ghj
Title1.75 Angstrom Crystal Structure of Transcriptional Regulator ftom Vibrio vulnificus.
ComponentsProbable transcriptional regulator
KeywordsTRANSCRIPTION / Structural Genomics / NIAID / National Institute of Allergy and Infectious Diseases / Center for Structural Genomics of Infectious Diseases / CSGID / Helix-turn-helix XRE-family like proteins / transcriptional regulator / DNA
Function / homology
Function and homology information


Helix-turn-helix / lambda repressor-like DNA-binding domains / Helix-turn-helix XRE-family like proteins / Cro/C1-type HTH domain profile. / Cro/C1-type helix-turn-helix domain / 434 Repressor (Amino-terminal Domain) / Lambda repressor-like, DNA-binding domain superfamily / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
Probable transcriptional regulator / Probable transcriptional regulator
Similarity search - Component
Biological speciesVibrio vulnificus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.75 Å
AuthorsMinasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Grimshaw, S. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
CitationJournal: TO BE PUBLISHED
Title: 1.75 Angstrom Crystal Structure of Transcriptional Regulator ftom Vibrio vulnificus.
Authors: Minasov, G. / Shuvalova, L. / Dubrovska, I. / Winsor, J. / Grimshaw, S. / Papazisi, L. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
History
DepositionAug 7, 2012Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 15, 2012Provider: repository / Type: Initial release
Revision 1.1Nov 15, 2017Group: Refinement description / Category: software / Item: _software.name
Revision 1.2Nov 6, 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 / 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 / _pdbx_entry_details.has_protein_modification / _struct_conn.pdbx_leaving_atom_flag / _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: Probable transcriptional regulator
B: Probable transcriptional regulator


Theoretical massNumber of molelcules
Total (without water)22,9372
Polymers22,9372
Non-polymers00
Water2,684149
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3090 Å2
ΔGint-25 kcal/mol
Surface area7980 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.742, 70.740, 35.746
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein Probable transcriptional regulator


Mass: 11468.505 Da / Num. of mol.: 2 / Fragment: Transcriptional Regulator
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio vulnificus (bacteria) / Strain: CMCP6 / Gene: VV1_2191 / Plasmid: pMCSG7 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21 / References: UniProt: Q8DAK3, UniProt: A0A3Q0L571*PLUS
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 149 / Source method: isolated from a natural source / Formula: H2O
Has protein modificationY
Sequence detailsTHE INITIAL SEQUENCE WAS CUT AFTER RESIDUE 77 OR MAYBE FEW RESIDUES AFTER

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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: 1.76 Å3/Da / Density % sol: 29.99 %
Crystal growTemperature: 295 K / Method: vapor diffusion, sitting drop / pH: 9
Details: Protein: 7.6mg/mL, 0.5M Sodium cloride, 0.01M Tris-HCl pH 8.3; Screen: PACT (D6), 0.1M MMT buffer pH 9.0, 25% (w/v) PEG 1500, VAPOR DIFFUSION, SITTING DROP, temperature 295K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Jul 20, 2012 / Details: Beryllium lenses
RadiationMonochromator: Diamond / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.75→30 Å / Num. all: 16622 / Num. obs: 16622 / % possible obs: 97.6 % / Observed criterion σ(I): -3 / Redundancy: 6.9 % / Biso Wilson estimate: 21.7 Å2 / Rmerge(I) obs: 0.095 / Net I/σ(I): 31.3
Reflection shellResolution: 1.75→1.78 Å / Redundancy: 5.8 % / Rmerge(I) obs: 0.482 / Mean I/σ(I) obs: 3.3 / Num. unique all: 713 / % possible all: 83.6

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Processing

Software
NameVersionClassification
Blu-IceMaxdata collection
PHENIXmodel building
REFMAC5.5.0102refinement
HKL-3000data reduction
HKL-3000data scaling
PHENIXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.75→28.53 Å / Cor.coef. Fo:Fc: 0.968 / Cor.coef. Fo:Fc free: 0.949 / SU B: 4.742 / SU ML: 0.064
Isotropic thermal model: Thermal Factors Individually Refined
Cross valid method: THROUGHOUT / ESU R: 0.122 / ESU R Free: 0.12 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.22341 847 5.1 %RANDOM
Rwork0.18157 ---
all0.18366 15662 --
obs0.18366 15662 97.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 21.626 Å2
Baniso -1Baniso -2Baniso -3
1--2.88 Å20 Å2-0 Å2
2--4.4 Å20 Å2
3----1.52 Å2
Refinement stepCycle: LAST / Resolution: 1.75→28.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1148 0 0 149 1297
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0221272
X-RAY DIFFRACTIONr_bond_other_d0.0010.02862
X-RAY DIFFRACTIONr_angle_refined_deg1.2271.991726
X-RAY DIFFRACTIONr_angle_other_deg0.81132147
X-RAY DIFFRACTIONr_dihedral_angle_1_deg2.8875171
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.07326.03853
X-RAY DIFFRACTIONr_dihedral_angle_3_deg9.89715264
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.816158
X-RAY DIFFRACTIONr_chiral_restr0.0770.2210
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.021433
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02219
X-RAY DIFFRACTIONr_mcbond_it1.1581.5816
X-RAY DIFFRACTIONr_mcbond_other0.3981.5325
X-RAY DIFFRACTIONr_mcangle_it1.90421326
X-RAY DIFFRACTIONr_scbond_it3.1763456
X-RAY DIFFRACTIONr_scangle_it5.1934.5400
LS refinement shellResolution: 1.75→1.795 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.262 49 -
Rwork0.299 994 -
obs-994 84.11 %
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)
11.417-0.03050.45041.3568-2.23525.0444-0.0682-0.4506-0.07180.0875-0.0438-0.1930.11660.24360.1120.17290.0012-0.01110.2692-0.00380.168942.08312.595853.9836
25.64670.90020.19331.23960.63857.00020.0543-0.2307-0.130.2369-0.2189-0.1374-0.2020.30980.16460.1857-0.00960.00830.1577-0.00430.19444.780611.328141.8837
33.25590.7022-0.75363.4246-0.71893.18760.0750.5204-0.1114-0.053-0.1377-0.07320.0475-0.04560.06270.0552-0.00460.00960.1143-0.02090.053943.464715.507430.2267
41.2064-0.02652.12053.5475-1.32114.2332-0.0090.16780.15070.1931-0.0155-0.2358-0.38810.2420.02460.2629-0.01350.06460.16720.01350.299942.251522.464939.7943
56.1213-1.8386-2.5786.57252.60984.33830.04650.3838-0.33560.0362-0.06320.17990.0755-0.2030.01680.01230.0015-0.02030.0726-0.03110.053633.815812.270135.7199
611.3936-7.0223-8.87437.0978-0.586315.3816-0.31740.306-0.3095-0.07360.04390.32830.6282-0.51550.27360.1979-0.04350.0040.018-0.00150.351425.7285.194144.4576
70.9498-1.0389-0.24070.79221.81528.54680.0490.2016-0.11750.059-0.23260.15720.4723-0.84010.18360.15990.00420.0080.32190.01420.174423.639412.848537.1623
84.9346-0.3531-1.11543.044-0.26834.707-0.1298-0.2309-0.3231-0.01220.07890.13870.3137-0.28690.05090.02650.00460.01510.12350.05070.04619.920612.364755.1348
93.7366-0.9585-2.09386.185-1.091310.9339-0.0443-0.86110.43050.09030.21220.0235-0.54620.0126-0.16790.0643-0.00160.00660.2937-0.08050.109325.858722.237458.3125
1012.2357-0.87992.75852.449-0.10660.6503-0.0698-0.14390.3406-0.1088-0.01820.1174-0.0733-0.03020.0880.12570.02590.00350.112-0.01650.091726.928721.037448.0134
113.90680.0788-0.84285.9883-1.49145.46580.0627-0.5093-0.25710.0989-0.11950.14160.09910.12070.05690.0138-0.0122-0.0030.09180.0360.051431.070111.533154.8916
1210.4947-1.1909-9.7166.49570.61412.517-0.2883-0.0717-0.31890.02780.1526-0.28380.41320.07590.13580.0899-0.0024-0.00710.00870.01040.164338.90985.011744.683
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A2 - 12
2X-RAY DIFFRACTION2A13 - 19
3X-RAY DIFFRACTION3A20 - 38
4X-RAY DIFFRACTION4A39 - 51
5X-RAY DIFFRACTION5A52 - 67
6X-RAY DIFFRACTION6A68 - 74
7X-RAY DIFFRACTION7B2 - 15
8X-RAY DIFFRACTION8B16 - 30
9X-RAY DIFFRACTION9B31 - 42
10X-RAY DIFFRACTION10B43 - 54
11X-RAY DIFFRACTION11B55 - 65
12X-RAY DIFFRACTION12B66 - 77

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