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- PDB-3frw: Crystal structure of putative TrpR protein from Ruminococcus obeum -

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Basic information

Entry
Database: PDB / ID: 3frw
TitleCrystal structure of putative TrpR protein from Ruminococcus obeum
ComponentsPutative Trp repressor protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / APC21159 / TrpR / Trp repressor / PSI-2 / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


sequence-specific DNA binding / DNA-binding transcription factor activity
Similarity search - Function
TrpR homologue YerC/YecD / TrpR-like / Trp repressor / TrpR-like superfamily / Trp repressor protein / Trp repressor/replication initiator / Trp Operon Repressor; Chain A / Orthogonal Bundle / Mainly Alpha
Similarity search - Domain/homology
ACETATE ION / TrpR family protein YerC/YecD
Similarity search - Component
Biological speciesRuminococcus obeum ATCC 29174 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.05 Å
AuthorsOsipiuk, J. / Keigher, L. / Jedrzejczak, R. / Babnigg, G. / Joachimiak, A. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be Published
Title: X-ray crystal structure of putative TrpR protein from Ruminococcus obeum.
Authors: Osipiuk, J. / Keigher, L. / Jedrzejczak, R. / Babnigg, G. / Joachimiak, A.
History
DepositionJan 8, 2009Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Nov 1, 2017Group: Refinement description / Category: software
Revision 1.3Jan 22, 2020Group: Database references / Derived calculations
Category: pdbx_struct_assembly / pdbx_struct_assembly_gen ...pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop / struct_conn / struct_ref_seq_dif
Item: _pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details ..._pdbx_struct_assembly.oligomeric_count / _pdbx_struct_assembly.oligomeric_details / _pdbx_struct_assembly_gen.asym_id_list / _pdbx_struct_assembly_prop.value / _struct_conn.pdbx_leaving_atom_flag / _struct_ref_seq_dif.details
Revision 1.4Nov 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_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _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: Putative Trp repressor protein
B: Putative Trp repressor protein
C: Putative Trp repressor protein
D: Putative Trp repressor protein
E: Putative Trp repressor protein
F: Putative Trp repressor protein
G: Putative Trp repressor protein
H: Putative Trp repressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)100,14911
Polymers99,9728
Non-polymers1773
Water7,837435
1
A: Putative Trp repressor protein
B: Putative Trp repressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0523
Polymers24,9932
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5610 Å2
ΔGint-42 kcal/mol
Surface area10590 Å2
MethodPISA
2
C: Putative Trp repressor protein
D: Putative Trp repressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0523
Polymers24,9932
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5360 Å2
ΔGint-41 kcal/mol
Surface area10230 Å2
MethodPISA
3
E: Putative Trp repressor protein
F: Putative Trp repressor protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)25,0523
Polymers24,9932
Non-polymers591
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5270 Å2
ΔGint-43 kcal/mol
Surface area10700 Å2
MethodPISA
4
G: Putative Trp repressor protein
H: Putative Trp repressor protein


Theoretical massNumber of molelcules
Total (without water)24,9932
Polymers24,9932
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area5030 Å2
ΔGint-39 kcal/mol
Surface area10300 Å2
MethodPISA
Unit cell
Length a, b, c (Å)67.601, 110.991, 77.262
Angle α, β, γ (deg.)90.000, 101.470, 90.000
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
Putative Trp repressor protein


Mass: 12496.508 Da / Num. of mol.: 8
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Ruminococcus obeum ATCC 29174 (bacteria)
Gene: RUMOBE_00155 / Plasmid: pMCSG19 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A5ZMD8
#2: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C2H3O2
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 435 / 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: 2.84 Å3/Da / Density % sol: 56.71 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 7.4
Details: 0.2 M Sodium acetate, 20% PEG 3350, pH 7.4, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 19-ID / Wavelength: 0.9792 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Dec 12, 2008
RadiationMonochromator: double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9792 Å / Relative weight: 1
ReflectionResolution: 2.05→42.3 Å / Num. all: 69539 / Num. obs: 69539 / % possible obs: 100 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 7.5 % / Biso Wilson estimate: 40.7 Å2 / Rmerge(I) obs: 0.105 / Χ2: 2.9 / Net I/σ(I): 34.781
Reflection shellResolution: 2.05→2.09 Å / Redundancy: 7.1 % / Rmerge(I) obs: 0.803 / Mean I/σ(I) obs: 3.37 / Num. unique all: 3446 / Χ2: 1.777 / % possible all: 100

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
REFMAC5.5.0054refinement
PDB_EXTRACT3.006data extraction
SBC-Collectdata collection
HKL-3000data reduction
HKL-3000data scaling
SHELXDphasing
MLPHAREphasing
DMphasing
SOLVEphasing
RESOLVEphasing
HKL-3000phasing
RefinementMethod to determine structure: SAD / Resolution: 2.05→42.3 Å / Cor.coef. Fo:Fc: 0.959 / Cor.coef. Fo:Fc free: 0.942 / Occupancy max: 1 / Occupancy min: 0.4 / SU B: 8.23 / SU ML: 0.1 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / ESU R: 0.158 / ESU R Free: 0.146 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: 1. HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. 2. U VALUES: RESIDUAL ONLY. 3. PROGRAM PHENIX HAS ALSO BEEN USED IN REFINEMENT.
RfactorNum. reflection% reflectionSelection details
Rfree0.218 3481 5 %RANDOM
Rwork0.18 ---
all0.182 69037 --
obs0.182 69037 99.13 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 63.58 Å2 / Biso mean: 26.259 Å2 / Biso min: 7.91 Å2
Baniso -1Baniso -2Baniso -3
1--1 Å20 Å2-0.11 Å2
2--1.95 Å20 Å2
3----1 Å2
Refinement stepCycle: LAST / Resolution: 2.05→42.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6104 0 12 435 6551
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0226414
X-RAY DIFFRACTIONr_angle_refined_deg1.4861.9718659
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8935824
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.21224.268321
X-RAY DIFFRACTIONr_dihedral_angle_3_deg17.134151293
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.1421552
X-RAY DIFFRACTIONr_chiral_restr0.1050.2990
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.024760
X-RAY DIFFRACTIONr_mcbond_it0.8771.53861
X-RAY DIFFRACTIONr_mcangle_it1.66526292
X-RAY DIFFRACTIONr_scbond_it3.02332553
X-RAY DIFFRACTIONr_scangle_it4.8194.52326
LS refinement shellResolution: 2.05→2.11 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.274 240 -
Rwork0.222 4594 -
all-4834 -
obs-4834 94.93 %
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)
13.6021-0.0335-1.84461.5618-0.27564.66570.01650.71450.031-0.2666-0.0215-0.10460.05610.09230.0050.05860.0144-0.01340.203-0.010.083560.795125.55299.4613
21.6489-0.187-0.31661.70052.03864.18820.00460.21830.00710.1003-0.12640.07980.0815-0.17070.12180.0211-0.0077-0.00020.04660.01920.051555.439527.742824.0513
30.86930.09992.06490.09740.32915.1322-0.1294-0.03160.0844-0.10950.0504-0.0209-0.4279-0.05460.07890.17060.00990.00970.1136-0.02230.093587.777335.417-8.4093
42.2348-1.3111.52671.6399-1.48974.5717-0.0322-0.14590.01240.04530.0658-0.1432-0.01720.2136-0.03360.0481-0.01320.00620.1627-0.05780.062493.809430.55835.6527
52.1542-0.9854-0.4042.46771.94662.2041-0.02050.0262-0.03790.17890.0926-0.09260.34250.143-0.07210.08050.00620.00630.22920.03970.090188.061736.667234.0594
65.2758-1.8585-0.53193.6023-0.34012.5987-0.00450.10751.08890.1077-0.00890.0439-0.43630.16740.01340.0751-0.0317-0.01980.16890.05580.304382.34850.893535.8695
70.71871.14830.11346.70870.43690.2599-0.06630.1057-0.0446-0.1810.0743-0.2888-0.03280.0128-0.00810.03190.0076-0.00230.0393-0.01990.040755.345269.164427.5773
80.92771.451-0.31946.452-2.050.7153-0.02760.0087-0.1645-0.18630.14260.32780.0959-0.0605-0.11510.05720.00210.02070.0536-0.01960.160849.718754.593631.2665
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A5 - 98
2X-RAY DIFFRACTION2B2 - 97
3X-RAY DIFFRACTION3C6 - 98
4X-RAY DIFFRACTION4D5 - 96
5X-RAY DIFFRACTION5E4 - 99
6X-RAY DIFFRACTION6F3 - 96
7X-RAY DIFFRACTION7G6 - 97
8X-RAY DIFFRACTION8H6 - 98

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