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Basic information

Entry
Database: PDB / ID: 2wj9
TitleArdB
ComponentsINTERGENIC-REGION PROTEIN
KeywordsHYDROLASE INHIBITOR / ANTIRESTRICTION
Function / homology
Function and homology information


endonuclease activity
Similarity search - Function
Antirestriction protein / Antirestriction protein / Antirestriction domain superfamily / Antirestriction protein / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
BETA-MERCAPTOETHANOL / Antirestriction protein
Similarity search - Component
Biological speciesEscherichia coli CFT073 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / Resolution: 1.62 Å
AuthorsWeikart, N.D. / Roberts, G. / Johnson, K.A. / Oke, M. / Cooper, L.P. / McMahon, S.A. / White, J.H. / Liu, H. / Carter, L.G. / Walkinshaw, M.D. ...Weikart, N.D. / Roberts, G. / Johnson, K.A. / Oke, M. / Cooper, L.P. / McMahon, S.A. / White, J.H. / Liu, H. / Carter, L.G. / Walkinshaw, M.D. / Blakely, G.W. / Naismith, J.H. / Dryden, D.T.F.
CitationJournal: J.Struct.Funct.Genomics / Year: 2010
Title: The Scottish Structural Proteomics Facility: Targets, Methods and Outputs.
Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / ...Authors: Oke, M. / Carter, L.G. / Johnson, K.A. / Liu, H. / Mcmahon, S.A. / Yan, X. / Kerou, M. / Weikart, N.D. / Kadi, N. / Sheikh, M.A. / Schmelz, S. / Dorward, M. / Zawadzki, M. / Cozens, C. / Falconer, H. / Powers, H. / Overton, I.M. / Van Niekerk, C.A.J. / Peng, X. / Patel, P. / Garrett, R.A. / Prangishvili C, D. / Botting, H. / Coote, P.J. / Dryden, D.T.F. / Barton, G.J. / Schwarz-Linek, U. / Challis, G.L. / Taylor, G.L. / White, M.F. / Naismith, J.H.
History
DepositionMay 25, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 18, 2010Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3May 2, 2018Group: Data collection / Source and taxonomy / Category: diffrn_source / entity_src_gen
Item: _diffrn_source.pdbx_synchrotron_beamline / _entity_src_gen.gene_src_strain ..._diffrn_source.pdbx_synchrotron_beamline / _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name / _entity_src_gen.pdbx_host_org_scientific_name

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: INTERGENIC-REGION PROTEIN
B: INTERGENIC-REGION PROTEIN
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,26013
Polymers41,2872
Non-polymers97311
Water3,261181
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area4940 Å2
ΔGint-84.6 kcal/mol
Surface area13080 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.900, 67.640, 80.610
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:
Dom-IDComponent-IDEns-IDRefine codeAuth asym-IDAuth seq-ID
1115A21 - 60
2115B21 - 60
1215A71 - 82
2215B71 - 82
1315A92 - 157
2315B92 - 157

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Components

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Protein , 1 types, 2 molecules AB

#1: Protein INTERGENIC-REGION PROTEIN / ARDB


Mass: 20643.508 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli CFT073 (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q8VRA1

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Non-polymers , 5 types, 192 molecules

#2: Chemical
ChemComp-BME / BETA-MERCAPTOETHANOL / 2-Mercaptoethanol


Mass: 78.133 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: C2H6OS
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL / 2-Methyl-2,4-pentanediol


Mass: 118.174 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#5: Chemical ChemComp-CL / CHLORIDE ION / Chloride


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#6: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 181 / Source method: isolated from a natural source / Formula: H2O

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Details

Nonpolymer detailsSULFATE (SO4): SULFATE ION CHLORIDE (CL): CHLORIDE ION BETA MERCAPTO ETHANOL (BME): COVALENT LINK ...SULFATE (SO4): SULFATE ION CHLORIDE (CL): CHLORIDE ION BETA MERCAPTO ETHANOL (BME): COVALENT LINK TO CYS RESIDUES, THINK ARISES DURING PURIFICATION METHANPENTANDIOL (MPD): METHANPENTANDIOL FROM SOLVENT

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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: 2.22 Å3/Da / Density % sol: 44.04 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-3 / Type: ESRF / Wavelength: 0.931
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.931 Å / Relative weight: 1
ReflectionResolution: 1.62→23 Å / Num. obs: 36476 / % possible obs: 93 % / Observed criterion σ(I): 0 / Redundancy: 2.9 % / Rmerge(I) obs: 0.05 / Net I/σ(I): 13
Reflection shellResolution: 1.62→1.71 Å / Redundancy: 2.8 % / Rmerge(I) obs: 0.4 / Mean I/σ(I) obs: 2.8 / % possible all: 97

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MIR
Starting model: NONE

Resolution: 1.62→80.58 Å / Cor.coef. Fo:Fc: 0.962 / Cor.coef. Fo:Fc free: 0.951 / SU B: 4.315 / SU ML: 0.073 / Cross valid method: THROUGHOUT / ESU R: 0.101 / ESU R Free: 0.097 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS.
RfactorNum. reflection% reflectionSelection details
Rfree0.21792 1934 5 %RANDOM
Rwork0.19136 ---
obs0.19264 36476 93.67 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 26.138 Å2
Baniso -1Baniso -2Baniso -3
1-2.32 Å20 Å20 Å2
2---1.99 Å20 Å2
3----0.34 Å2
Refinement stepCycle: LAST / Resolution: 1.62→80.58 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2253 0 55 181 2489
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0222440
X-RAY DIFFRACTIONr_bond_other_d0.0080.021617
X-RAY DIFFRACTIONr_angle_refined_deg1.2411.9453327
X-RAY DIFFRACTIONr_angle_other_deg0.9013.0033894
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.7765298
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.74823.363113
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.2315370
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.3711516
X-RAY DIFFRACTIONr_chiral_restr0.1590.2353
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.022685
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02509
X-RAY DIFFRACTIONr_nbd_refined0.2060.2485
X-RAY DIFFRACTIONr_nbd_other0.1860.21583
X-RAY DIFFRACTIONr_nbtor_refined0.1730.21162
X-RAY DIFFRACTIONr_nbtor_other0.0850.21087
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1480.2108
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2220.221
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2430.245
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.3260.217
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.8461.51887
X-RAY DIFFRACTIONr_mcbond_other0.1221.5579
X-RAY DIFFRACTIONr_mcangle_it0.77622348
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.38431180
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.7114.5971
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Dom-IDAuth asym-IDNumberTypeRms dev position (Å)Weight position
1A676medium positional0.190.5
2B676medium positional0.190.5
1A875loose positional0.595
2B875loose positional0.595
1A676medium thermal0.612
2B676medium thermal0.612
1A875loose thermal1.0210
2B875loose thermal1.0210
LS refinement shellResolution: 1.62→1.662 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.332 146 -
Rwork0.284 2758 -
obs--97.61 %
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)
11.4766-0.0592-0.9223.6402-0.01381.5412-0.05170.1479-0.0375-0.24120.00690.02530.1125-0.12830.0448-0.1399-0.03190.0114-0.0639-0.0024-0.1356-23.5655.442-1.544
21.1853-0.0881-0.42572.4039-0.05041.7616-0.0421-0.0644-0.03140.16990.02650.15270.0885-0.05160.0156-0.17860.00210.0055-0.1429-0.0009-0.1397-34.50915.62522.058
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A9 - 157
2X-RAY DIFFRACTION2B8 - 157
3X-RAY DIFFRACTION2A1162

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