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- PDB-4uds: Crystal structure of MbdR regulator from Azoarcus sp. CIB -

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Basic information

Entry
Database: PDB / ID: 4uds
TitleCrystal structure of MbdR regulator from Azoarcus sp. CIB
ComponentsMBDR REGULATOR
KeywordsTRANSCRIPTION / TETR FAMILY
Function / homologyTetracycline Repressor, domain 2 / Tetracycline Repressor; domain 2 / Orthogonal Bundle / Mainly Alpha
Function and homology information
Biological speciesAZOARCUS SP. CIB (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.76 Å
AuthorsLiu, H. / Liu, H.X. / MacMahon, S.A. / Juarez, J.F. / Zamarro, M.T. / Eberlein, C. / Boll, M. / Carmona, M. / Diaz, E. / Naismith, J.H.
CitationJournal: J.Biol.Chem. / Year: 2015
Title: Unraveling the Specific Regulation of the Mbd Central Pathway for the Anaerobic Degradation of 3-Methylbenzoate.
Authors: Juarez, J.F. / Liu, H. / Zamarro, M.T. / Mcmahon, S. / Liu, H. / Naismith, J.H. / Eberlein, C. / Boll, M. / Carmona, M. / Diaz, E.
History
DepositionDec 11, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Dec 24, 2014Provider: repository / Type: Initial release
Revision 1.1Apr 1, 2015Group: Database references
Revision 1.2May 27, 2015Group: Database references
Revision 1.3Sep 13, 2017Group: Data collection / Category: diffrn_detector / Item: _diffrn_detector.type
Revision 1.4Oct 23, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_entry_details / pdbx_modification_feature / struct_conn
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: MBDR REGULATOR


Theoretical massNumber of molelcules
Total (without water)24,2411
Polymers24,2411
Non-polymers00
Water3,747208
1
A: MBDR REGULATOR

A: MBDR REGULATOR


Theoretical massNumber of molelcules
Total (without water)48,4822
Polymers48,4822
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_555-x,-y,z1
Buried area5370 Å2
ΔGint-27.9 kcal/mol
Surface area15510 Å2
MethodPISA
Unit cell
Length a, b, c (Å)47.030, 56.210, 143.820
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222
Components on special symmetry positions
IDModelComponents
11A-2158-

HOH

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Components

#1: Protein MBDR REGULATOR


Mass: 24240.928 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) AZOARCUS SP. CIB (bacteria) / Production host: ESCHERICHIA COLI (E. coli)
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 208 / 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

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Sample preparation

CrystalDensity Matthews: 1.96 Å3/Da / Density % sol: 37.26 % / Description: NONE

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I03 / Wavelength: 0.9793
DetectorType: DECTRIS PILATUS3 6M / Detector: PIXEL
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9793 Å / Relative weight: 1
ReflectionResolution: 1.76→52.35 Å / Num. obs: 17349 / % possible obs: 95.7 % / Observed criterion σ(I): 4.1 / Redundancy: 7 % / Rmerge(I) obs: 0.07

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Processing

SoftwareName: REFMAC / Version: 5.6.0111 / Classification: refinement
RefinementMethod to determine structure: MAD
Starting model: NONE

Resolution: 1.76→52.35 Å / Cor.coef. Fo:Fc: 0.937 / Cor.coef. Fo:Fc free: 0.897 / SU B: 5.834 / SU ML: 0.095 / Cross valid method: THROUGHOUT / ESU R: 0.14 / ESU R Free: 0.143 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT
RfactorNum. reflection% reflectionSelection details
Rfree0.24948 938 5.1 %RANDOM
Rwork0.19069 ---
obs0.1936 17349 94.08 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Refinement stepCycle: LAST / Resolution: 1.76→52.35 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1469 0 0 208 1677
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0230.0221517
X-RAY DIFFRACTIONr_bond_other_d0.0010.021020
X-RAY DIFFRACTIONr_angle_refined_deg1.8181.9762052
X-RAY DIFFRACTIONr_angle_other_deg1.07932496
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.2135194
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.97123.90664
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.37615276
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.3271510
X-RAY DIFFRACTIONr_chiral_restr0.1070.2240
X-RAY DIFFRACTIONr_gen_planes_refined0.0090.021678
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02303
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_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
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
LS refinement shellResolution: 1.758→1.804 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.268 51 -
Rwork0.207 899 -
obs--68.25 %
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)
14.99313.8891-0.73733.50150.04463.06160.02670.14570.08080.00210.14970.0161-0.0494-0.066-0.17630.0197-0.00710.00630.05080.02380.02426.8799.756.283
20.1730.4085-0.91951.0537-1.90135.89020.0142-0.0006-0.0097-0.10740.1295-0.0601-0.26880.4309-0.14370.1531-0.11570.0150.1842-0.08620.068814.2339.9471.506
30.36160.25331.8510.46051.142710.3852-0.03290.0094-0.0071-0.0077-0.0112-0.1079-0.05260.02970.04410.0253-0.01590.00420.0649-0.01210.046818.7547.03826.532
40.9913-1.26443.7275.4187-6.956715.29070.0128-0.0072-0.03780.07610.12690.0307-0.0139-0.0939-0.13970.0282-0.00590.00480.0343-0.0070.042611.5748.6834.846
51.35350.47540.70664.10742.09841.4228-0.00660.0559-0.0243-0.12990.0982-0.0856-0.0669-0.0446-0.09160.0348-0.01440.01920.08220.00570.03716.2473.13817.035
69.5594-2.72076.34460.8101-2.4716.65940.28230.3458-0.0648-0.1109-0.12450.02160.60610.5282-0.15780.16960.0550.05790.03920.00320.058112.91-5.07912.742
70.96860.1266-1.40740.9732-2.13566.0824-0.023-0.0160.01350.01340.0473-0.03010.0137-0.0199-0.02430.01030.0035-0.02430.0786-0.05550.10614.181-3.48335.532
82.6723-1.19813.12141.0697-3.21889.94830.19180.0157-0.3544-0.0630.02950.11660.16050.023-0.22130.0170.0134-0.01240.12790.02960.10197.365-7.36736.848
90.7946-0.4948-0.07923.3171-1.37481.81760.0534-0.0130.0439-0.019-0.0574-0.09-0.0917-0.07880.0040.0343-0.00550.00220.05670.00020.0246-1.8617.32324.003
100.1273-0.67670.41314.4375-3.59953.7667-0.01530.00620.06220.1443-0.0684-0.2375-0.17640.02910.08370.0380.01020.00360.038-0.01610.0702-0.8339.3735.808
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A18 - 40
2X-RAY DIFFRACTION2A41 - 65
3X-RAY DIFFRACTION3A66 - 87
4X-RAY DIFFRACTION4A88 - 106
5X-RAY DIFFRACTION5A107 - 123
6X-RAY DIFFRACTION6A124 - 134
7X-RAY DIFFRACTION7A135 - 157
8X-RAY DIFFRACTION8A158 - 170
9X-RAY DIFFRACTION9A171 - 184
10X-RAY DIFFRACTION10A185 - 205

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