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- PDB-3brj: Crystal structure of mannitol operon repressor (MtlR) from Vibrio... -

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Basic information

Entry
Database: PDB / ID: 3brj
TitleCrystal structure of mannitol operon repressor (MtlR) from Vibrio parahaemolyticus RIMD 2210633
ComponentsMannitol operon repressor
KeywordsTRANSCRIPTION / APC85967.1 / mannitol operon repressor / MtlR / Vibrio parahaemolyticus RIMD 2210633 / structural genomics / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homologyMannitol repressor MtlR-like / MtlR-like superfamily / Mannitol repressor / Nucleotidyltransferases domain 2 / Four Helix Bundle (Hemerythrin (Met), subunit A) / negative regulation of DNA-templated transcription / Up-down Bundle / Mainly Alpha / Mannitol operon repressor
Function and homology information
Biological speciesVibrio parahaemolyticus RIMD 2210633 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.75 Å
AuthorsTan, K. / Zhou, M. / Moy, S. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: J.Biol.Chem. / Year: 2009
Title: The mannitol operon repressor MtlR belongs to a new class of transcription regulators in bacteria.
Authors: Tan, K. / Clancy, S. / Borovilos, M. / Zhou, M. / Horer, S. / Moy, S. / Volkart, L.L. / Sassoon, J. / Baumann, U. / Joachimiak, A.
History
DepositionDec 21, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 15, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Oct 30, 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 / struct_site
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 / _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: Mannitol operon repressor
B: Mannitol operon repressor
C: Mannitol operon repressor
D: Mannitol operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)79,6939
Polymers79,3524
Non-polymers3405
Water54030
1
A: Mannitol operon repressor
B: Mannitol operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8925
Polymers39,6762
Non-polymers2163
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1580 Å2
MethodPISA
2
C: Mannitol operon repressor
D: Mannitol operon repressor
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,8004
Polymers39,6762
Non-polymers1242
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area1550 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.281, 63.281, 227.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number76
Space group name H-MP41

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Components

#1: Protein
Mannitol operon repressor


Mass: 19838.082 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Vibrio parahaemolyticus RIMD 2210633 (bacteria)
Species: Vibrio parahaemolyticus / Strain: RIMD 2210633 / Serotype O3:K6 / Gene: VP0368 / Plasmid: pMCSG7 / Species (production host): Escherichia coli / Production host: Escherichia coli BL21 (bacteria) / Strain (production host): BL21 / References: UniProt: Q87SQ4
#2: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 30 / 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: 2.87 Å3/Da / Density % sol: 57.07 %
Crystal growTemperature: 289 K / Method: vapor diffusion, hanging drop / pH: 7
Details: 0.2M tri-Ammonium citrate, 20% w/v PEG 3350, pH 7.0, VAPOR DIFFUSION, HANGING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.97927, 0.97941
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Feb 12, 2007 / Details: Mirrors
RadiationMonochromator: Si 111 crystal / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.979271
20.979411
ReflectionResolution: 2.75→48.56 Å / Num. all: 23045 / Num. obs: 23045 / % possible obs: 99.2 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.8 % / Rmerge(I) obs: 0.1 / Net I/σ(I): 17.5
Reflection shellResolution: 2.75→2.83 Å / Redundancy: 2.7 % / Rmerge(I) obs: 0.642 / Mean I/σ(I) obs: 1.5 / Num. unique all: 1732 / % possible all: 91.6

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: MAD / Resolution: 2.75→48.56 Å / Cor.coef. Fo:Fc: 0.942 / Cor.coef. Fo:Fc free: 0.902 / SU B: 30.374 / SU ML: 0.283 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 2.323 / ESU R Free: 0.379 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.27272 1178 5.1 %RANDOM
Rwork0.20679 ---
all0.21007 21778 --
obs0.21007 21778 99.14 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 51.545 Å2
Baniso -1Baniso -2Baniso -3
1--0.13 Å20 Å20 Å2
2---0.13 Å20 Å2
3---0.27 Å2
Refinement stepCycle: LAST / Resolution: 2.75→48.56 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5304 0 22 30 5356
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0225405
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.997294
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.0685664
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.16626.09266
X-RAY DIFFRACTIONr_dihedral_angle_3_deg24.867151016
X-RAY DIFFRACTIONr_dihedral_angle_4_deg23.1141524
X-RAY DIFFRACTIONr_chiral_restr0.1440.2846
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024016
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.2750.22748
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3370.23753
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1690.2196
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2750.275
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1220.24
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.12323385
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.85335394
X-RAY DIFFRACTIONr_scbond_it1.10422165
X-RAY DIFFRACTIONr_scangle_it1.72531899
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.75→2.82 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.403 94 -
Rwork0.329 1443 -
obs-1537 90.79 %
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)
17.2462-4.65180.90576.8477-2.26333.4215-0.2526-0.7485-0.19591.0920.35970.2174-0.188-0.2384-0.1070.15890.02790.1122-0.22250.0565-0.320132.024-6.534158.149
25.4253-4.35231.66575.1197-2.41232.435-0.1728-0.2846-0.25630.3336-0.00750.3087-0.2003-0.13690.1803-0.13830.05780.0816-0.133-0.0417-0.07944.65924.485137.896
36.9168-4.1601-1.3447.28180.563.5260.4430.61810.7561-1.0334-0.4246-0.0299-0.5817-0.3349-0.0184-0.02290.1247-0.0277-0.02820.1285-0.218725.66526.766117.768
42.4675-2.27990.28867.3335-2.11772.6545-0.0517-0.0221-0.1628-0.0566-0.1025-0.64470.11160.27250.1542-0.27120.02830.0123-0.16740.0229-0.296744.548-11.39132.855
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA6 - 1729 - 175
2X-RAY DIFFRACTION2BB4 - 1727 - 175
3X-RAY DIFFRACTION3CC6 - 1729 - 175
4X-RAY DIFFRACTION4DD5 - 1728 - 175

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