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- PDB-3opf: Crystal structure of TTHA0988 in space group P212121 -

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Basic information

Entry
Database: PDB / ID: 3opf
TitleCrystal structure of TTHA0988 in space group P212121
ComponentsPutative uncharacterized protein TTHA0988
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / KipI / KipA / cyclophilin / allophanate hydrolase / RIKEN Structural Genomics/Proteomics Initiative / RSGI / NPPSFA / National Project on Protein Structural and Functional Analyses
Function / homology
Function and homology information


hydrolase activity / ATP binding
Similarity search - Function
KipI family / Carboxyltransferase domain, subdomain A and B / Carboxyltransferase domain, subdomain A and B / Allophanate hydrolase subunit 2 / Carboxyltransferase domain, subdomain C and D / Carboxyltransferase domain, subdomain C and D / Allophanate hydrolase subunit 1 / Gyrase A; domain 2 - #40 / Cyclophilin-like / Cyclophilin ...KipI family / Carboxyltransferase domain, subdomain A and B / Carboxyltransferase domain, subdomain A and B / Allophanate hydrolase subunit 2 / Carboxyltransferase domain, subdomain C and D / Carboxyltransferase domain, subdomain C and D / Allophanate hydrolase subunit 1 / Gyrase A; domain 2 - #40 / Cyclophilin-like / Cyclophilin / Cyclophilin-like domain superfamily / Gyrase A; domain 2 / Beta Barrel / 2-Layer Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 1.95 Å
AuthorsJacques, D.A. / Kuramitsu, S. / Yokoyama, S. / Trewhella, J. / Guss, J.M. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: Acta Crystallogr.,Sect.D / Year: 2011
Title: The structure of TTHA0988 from Thermus thermophilus, a KipI-KipA homologue incorrectly annotated as an allophanate hydrolase
Authors: Jacques, D.A. / Langley, D.B. / Kuramitsu, S. / Yokoyama, S. / Trewhella, J. / Guss, J.M.
History
DepositionSep 1, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Feb 2, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / 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 uncharacterized protein TTHA0988
B: Putative uncharacterized protein TTHA0988
C: Putative uncharacterized protein TTHA0988
hetero molecules


Theoretical massNumber of molelcules
Total (without water)160,12910
Polymers159,4723
Non-polymers6577
Water20,8791159
1
A: Putative uncharacterized protein TTHA0988
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,4384
Polymers53,1571
Non-polymers2803
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Putative uncharacterized protein TTHA0988
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3463
Polymers53,1571
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Putative uncharacterized protein TTHA0988
hetero molecules


Theoretical massNumber of molelcules
Total (without water)53,3463
Polymers53,1571
Non-polymers1882
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)74.505, 132.107, 177.833
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Putative uncharacterized protein TTHA0988


Mass: 53157.391 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Gene: TTHA0988 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta2 / References: UniProt: Q5SJM0
#2: Chemical
ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C3H8O3
#3: Chemical ChemComp-SO4 / SULFATE ION / Sulfate


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1159 / Source method: isolated from a natural source / Formula: H2O

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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: 2.74 Å3/Da / Density % sol: 55.17 % / Mosaicity: 0.185 °
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 0.17M ammonium sulfate, 0.085M sodium cacodylate, 25.5% PEG 8000, 15% glycerol, pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL44B2 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Dec 1, 2004
RadiationMonochromator: Double crystal (Si111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. all: 111600 / Num. obs: 111600 / % possible obs: 87.3 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.5 % / Biso Wilson estimate: 26.7 Å2 / Rmerge(I) obs: 0.131 / Χ2: 1.028 / Net I/σ(I): 11.3
Reflection shell
Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique allΧ2% possible all
1.95-1.984.20.6062.332501.09451.6
1.98-2.024.30.542.635841.08256.6
2.02-2.064.30.4922.940161.0963.8
2.06-2.14.30.4433.247081.08174.4
2.1-2.154.40.4123.555591.06787.8
2.15-2.24.40.3673.855191.03286.9
2.2-2.254.40.3464.155291.08587.5
2.25-2.314.30.3174.455891.07588
2.31-2.384.30.2944.656331.0888.8
2.38-2.464.20.2684.857181.06690.2
2.46-2.544.20.244558781.04592.2
2.54-2.654.20.2245.160161.00894.5
2.65-2.774.20.1965.761471.00896.4
2.77-2.914.30.1796.262390.95198
2.91-3.14.50.1617.662821.0598.1
3.1-3.334.70.1468.563321.00198.8
3.33-3.674.90.1299.663540.98698.6
3.67-4.250.11310.863610.9998.3
4.2-5.2950.0991264310.94898.2
5.29-504.80.0715.964550.97794.9

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Phasing

PhasingMethod: molecular replacement
Phasing MRRfactor: 51.14 / Model details: Phaser MODE: MR_AUTO
Highest resolutionLowest resolution
Rotation2.31 Å33.05 Å
Translation2.31 Å33.05 Å

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Processing

Software
NameVersionClassificationNB
DENZOdata reduction
SCALEPACKdata scaling
PHASER2.1.4phasing
REFMACrefinement
PDB_EXTRACT3.1data extraction
ADSCQuantumdata collection
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3ORE
Resolution: 1.95→33.05 Å / Cor.coef. Fo:Fc: 0.952 / Cor.coef. Fo:Fc free: 0.937 / WRfactor Rfree: 0.2333 / WRfactor Rwork: 0.1972 / Occupancy max: 1 / Occupancy min: 0.5 / FOM work R set: 0.8511 / SU B: 8.034 / SU ML: 0.104 / SU R Cruickshank DPI: 0.1914 / SU Rfree: 0.1657 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R Free: 0.166 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES: RESIDUAL ONLY
RfactorNum. reflection% reflectionSelection details
Rfree0.2333 5548 5 %RANDOM
Rwork0.1972 ---
all0.199 110890 --
obs0.199 110890 86.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso max: 71.03 Å2 / Biso mean: 38.991 Å2 / Biso min: 12.55 Å2
Baniso -1Baniso -2Baniso -3
1-0.71 Å20 Å20 Å2
2---4.02 Å20 Å2
3---3.31 Å2
Refinement stepCycle: LAST / Resolution: 1.95→33.05 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms11026 0 39 1159 12224
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.02211404
X-RAY DIFFRACTIONr_bond_other_d0.0010.028186
X-RAY DIFFRACTIONr_angle_refined_deg1.1072.02715581
X-RAY DIFFRACTIONr_angle_other_deg0.785319785
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.50451472
X-RAY DIFFRACTIONr_dihedral_angle_2_deg31.50821.002439
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.364151644
X-RAY DIFFRACTIONr_dihedral_angle_4_deg12.79715133
X-RAY DIFFRACTIONr_chiral_restr0.0620.21689
X-RAY DIFFRACTIONr_gen_planes_refined0.0040.02212802
X-RAY DIFFRACTIONr_gen_planes_other0.0010.022367
X-RAY DIFFRACTIONr_mcbond_it1.16127361
X-RAY DIFFRACTIONr_mcbond_other0.33622940
X-RAY DIFFRACTIONr_mcangle_it1.859311758
X-RAY DIFFRACTIONr_scbond_it2.73144043
X-RAY DIFFRACTIONr_scangle_it4.18663820
LS refinement shellResolution: 1.951→2.002 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.285 240 -
Rwork0.257 4500 -
all-4740 -
obs--50.62 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL112)L122)L132)L222)L232)L332)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T112)T122)T132)T222)T232)T332)Origin x (Å)Origin y (Å)Origin z (Å)
12.05660.4876-0.42313.7960.61362.8235-0.0363-0.2324-0.24570.46250.0422-0.4130.46420.3627-0.0060.220.1073-0.07590.22620.03380.082741.28316.65718.9627
20.5740.1871-0.33661.72860.46571.5229-0.0546-0.03950.004-0.05850.0924-0.0785-0.02350.1076-0.03790.0215-0.02020.00120.12-0.02160.02836.905337.92132.6181
30.6850.20650.06881.46280.3940.4904-0.12330.0345-0.1017-0.07220.07080.02150.01440.00970.05250.071-0.00630.04190.1130.00370.032820.67423.0692-2.3983
41.70380.9976-0.35361.7620.04541.08330.0467-0.15520.06770.2881-0.06210.1084-0.04460.04240.01540.14930.05110.02420.15110.0050.00817.835118.944719.5243
52.4303-0.38810.33163.1327-0.11022.65750.05460.31830.0391-0.42770.0663-0.21170.01680.2361-0.12090.17430.01550.0170.1989-0.04530.02963.6453-3.865544.9309
60.84640.2137-0.18051.3606-0.25030.70990.0224-0.0212-0.01490.03540.01580.0462-0.00680.0494-0.03820.07520.0006-0.01320.1495-0.02040.00959.4342-2.137371.8253
70.8745-0.48460.71681.8311-0.26981.6939-0.055-0.01190.0756-0.05070.01850.0606-0.2395-0.19530.03650.11910.0274-0.01820.14870.01050.017343.446421.782646.2676
81.8067-0.17180.91982.257-0.17471.35080.04590.0484-0.1563-0.20350.12320.35430.1559-0.1229-0.16910.1173-0.056-0.05130.16070.01420.07439.8289-5.300946.8293
91.7559-0.5328-0.50173.47720.78233.83960.0025-0.1480.00020.13660.0313-0.3948-0.27610.2068-0.03390.1342-0.03570.02930.09550.01510.087890.5357-18.011116.2515
101.55870.6311-0.36561.77290.2821.2577-0.04070.13840.1341-0.18550.08430.2683-0.195-0.0454-0.04370.12060.0264-0.01540.09910.04390.058382.0722-40.54882.0033
110.9763-0.9151-0.71432.00770.612.3385-0.168-0.0997-0.21430.1276-0.10540.25490.0207-0.07940.27340.09580.01430.04070.1312-0.02320.066865.4172-29.090634.5691
122.2069-0.6077-0.43481.4463-0.42891.2491-0.19850.04650.328-0.08460.0752-0.1889-0.2624-0.10790.12320.27210.0594-0.0640.1268-0.01710.082367.0698-14.680211.4402
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 70
2X-RAY DIFFRACTION2A71 - 210
3X-RAY DIFFRACTION3A211 - 386
4X-RAY DIFFRACTION4A387 - 493
5X-RAY DIFFRACTION5B1 - 70
6X-RAY DIFFRACTION6B71 - 210
7X-RAY DIFFRACTION7B211 - 386
8X-RAY DIFFRACTION8B387 - 493
9X-RAY DIFFRACTION9C1 - 70
10X-RAY DIFFRACTION10C76 - 210
11X-RAY DIFFRACTION11C211 - 386
12X-RAY DIFFRACTION12C387 - 493

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