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- PDB-2ejq: Conserved hypothetical protein (TTHA0227) from Thermo thermophilus HB8 -

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Basic information

Entry
Database: PDB / ID: 2ejq
TitleConserved hypothetical protein (TTHA0227) from Thermo thermophilus HB8
ComponentsHypothetical protein TTHA0227
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / hypothetical protein / NPPSFA / National Project on Protein Structural and Functional Analyses / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homologyZincin-like - #20 / Zincin-like metallopeptidase / Zincin-like metallopeptidase superfamily / Zincin-like metallopeptidase / Zincin-like / 2-Layer Sandwich / metal ion binding / Alpha Beta / Uncharacterized protein
Function and homology information
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.08 Å
AuthorsRehse, P.H. / Yokoyama, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Conserved hypothetical protein (TTHA0227) from Thermo thermophilus HB8
Authors: Rehse, P.H. / Yokoyama, S.
History
DepositionMar 20, 2007Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Sep 25, 2007Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 10, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_asym_id / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_asym_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr1_symmetry / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details
Revision 1.3Apr 3, 2024Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Hypothetical protein TTHA0227
B: Hypothetical protein TTHA0227
hetero molecules


Theoretical massNumber of molelcules
Total (without water)29,6593
Polymers29,6352
Non-polymers241
Water2,000111
1
A: Hypothetical protein TTHA0227


Theoretical massNumber of molelcules
Total (without water)14,8171
Polymers14,8171
Non-polymers00
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Hypothetical protein TTHA0227
hetero molecules


Theoretical massNumber of molelcules
Total (without water)14,8422
Polymers14,8171
Non-polymers241
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)46.509, 63.281, 98.047
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 Hypothetical protein TTHA0227


Mass: 14817.395 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Gene: HB8 / Plasmid: pET-11a / Production host: Escherichia coli (E. coli) / Strain (production host): Rosseta834 (DE3) / References: UniProt: Q5SLR6
#2: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 111 / 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: 2

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Sample preparation

Crystal
IDDensity Matthews (Å3/Da)Density % sol (%)
12.4349.45
2
Crystal grow
Temperature (K)Crystal-IDMethodpHDetails
2931vapor diffusion, sitting drop7.21.2M Ammonium tartrate, 0.1M Bis-Tris Propane, pH 7.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K
2932vapor diffusion, sitting drop70.075 Bis-Tris Propane, 1M Succinic acid, 2% 2-propanol, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11001
21001
31
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONSPring-8 BL26B211
SYNCHROTRONSPring-8 BL26B220.97915, 0.97972, 0.9000
Detector
TypeIDDetectorDateDetails
ADSC QUANTUM 2101CCDMay 22, 2006mirrors
ADSC QUANTUM 2102CCDOct 2, 2006mirrors
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1Si (111)SINGLE WAVELENGTHMx-ray1
2Si (111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
111
20.979151
30.979721
40.91
Reflection

Χ2: 1 / D res low: 50 Å / Redundancy: 6.8 %

IDAv σ(I) over netINumberRmerge(I) obsD res high (Å)Num. obs% possible obs
119907610.0632.31333797.4
218.8903420.0582.31330197.4
317871610.0952.311286197.3
Diffraction reflection shell

Chi squared: 1

Highest resolution (Å)Lowest resolution (Å)% possible obs (%)IDRmerge(I) obsRedundancyRejects
4.955098.110.0495.9666
3.934.9599.510.0376.5181
3.443.9378.310.0495.245
3.123.4499.810.055710
2.93.1299.910.0787.12
2.732.999.910.1277.25
2.592.7399.910.1857.26
2.482.5999.710.2567.32
2.382.4899.810.3627.37
2.32.3899.510.4687.35
4.955098.120.0435.9666
3.934.9599.620.0346.5181
3.443.9377.720.0485.145
3.123.4499.920.0526.910
2.93.1299.920.0787.12
2.732.999.820.1237.25
2.592.7399.920.1867.26
2.482.5999.820.267.32
2.382.4899.820.3527.37
2.32.3899.520.4617.25
4.985099.430.1476.1666
3.954.9899.630.0336.6181
3.453.9574.630.0514.545
3.133.4599.830.0586.910
2.913.1310030.08572
2.742.9110030.1347.15
2.62.7499.830.2087.26
2.492.699.930.2647.32
2.392.4999.830.367.37
2.312.3999.930.4847.35
ReflectionResolution: 2.08→37.5 Å / Num. all: 18013 / Num. obs: 17938 / % possible obs: 99.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 6.85 % / Rmerge(I) obs: 0.048 / Χ2: 0.95 / Net I/σ(I): 21.8 / Scaling rejects: 929
Reflection shellResolution: 2.08→2.15 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.305 / Mean I/σ(I) obs: 4.6 / Num. measured all: 11770 / Num. unique all: 1755 / Χ2: 0.7 / % possible all: 99.9

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Phasing

PhasingMethod: MAD
Phasing set
ID
1
2
3
Phasing MAD set
Clust-IDExpt-IDSet-IDWavelength (Å)F double prime refinedF prime refined
13 wavelength10.97914.92-6.8
13 wavelength20.93.38-3.55
13 wavelength30.97973.04-8.54
Phasing MAD set site
IDAtom type symbolB isoFract xFract yFract zOccupancy
1Se52.6110.3190.5430.1061.265
2Se41.3330.8230.2890.1210.963
Phasing dmFOM : 0.67 / FOM acentric: 0.66 / FOM centric: 0.7 / Reflection: 9078 / Reflection acentric: 7688 / Reflection centric: 1390
Phasing dm shell
Resolution (Å)FOM FOM acentricFOM centricReflectionReflection acentricReflection centric
7.4-19.8940.910.930.86432277155
4.6-7.40.890.90.8613201023297
3.7-4.60.860.870.8214901256234
3.3-3.70.780.790.7413691185184
2.8-3.30.570.570.5527922446346
2.6-2.80.320.310.3416751501174

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Processing

Software
NameVersionClassificationNB
d*TREK8.0SSIdata scaling
SOLVE2.1phasing
RESOLVE2.1phasing
CNSrefinement
PDB_EXTRACT2data extraction
CrystalCleardata collection
d*TREKdata reduction
RefinementMethod to determine structure: MAD
Starting model: model derived from Se-MAD experiment transfered to higher resolution Native data set after single rebuilding cycle

Resolution: 2.08→37.48 Å / Isotropic thermal model: anisotropic / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.251 866 4.8 %random
Rwork0.235 ---
all0.235 18013 --
obs0.235 17938 99.6 %-
Solvent computationBsol: 55.301 Å2
Displacement parametersBiso mean: 57.291 Å2
Baniso -1Baniso -2Baniso -3
1--11.942 Å20 Å20 Å2
2---1.423 Å20 Å2
3---13.365 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.31 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.35 Å
Refinement stepCycle: LAST / Resolution: 2.08→37.48 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1814 0 1 111 1926
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008851.5
X-RAY DIFFRACTIONc_angle_d1.411762
X-RAY DIFFRACTIONc_dihedral_angle_d22.254772
X-RAY DIFFRACTIONc_improper_angle_d0.891982.5
LS refinement shellResolution: 2.08→2.15 Å
RfactorNum. reflection% reflection
Rfree0.3335 83 -
Rwork0.3466 --
obs-1755 99.9 %
Xplor file
Refine-IDSerial noParam file
X-RAY DIFFRACTION1CNS_TOPPAR:protein_rep.param
X-RAY DIFFRACTION2CNS_TOPPAR:water_rep.param
X-RAY DIFFRACTION3CNS_TOPPAR:ion.param

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