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- PDB-2cv9: Crystal structure of a hypothetical protein from Thermus thermoph... -

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Basic information

Entry
Database: PDB / ID: 2cv9
TitleCrystal structure of a hypothetical protein from Thermus thermophilus HB8
Componentshypothetical protein TTHA0625
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / beta alpha beta motif / RIKEN Structural Genomics/Proteomics Initiative / RSGI
Function / homology
Function and homology information


2',3'-cyclic-nucleotide 3'-phosphodiesterase activity / metal ion binding
Similarity search - Function
Metallophosphoesterase, YmdB-like / YmdB-like protein / Capsule synthesis protein, CapA / Bacterial capsule synthesis protein PGA_cap / Metallo-dependent phosphatases / Purple Acid Phosphatase; chain A, domain 2 / Metallo-dependent phosphatase-like / 4-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Capsule synthesis protein CapA domain-containing protein
Similarity search - Component
Biological speciesThermus thermophilus (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.5 Å
AuthorsKanagawa, M. / Yokoyama, S. / Kuramitsu, S. / RIKEN Structural Genomics/Proteomics Initiative (RSGI)
CitationJournal: To be Published
Title: Crystal structure of a hypothetical protein from Thermus thermophilus HB8
Authors: Kanagawa, M. / Yokoyama, S. / Kuramitsu, S.
History
DepositionJun 1, 2005Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Dec 1, 2005Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Source and taxonomy / Version format compliance
Revision 1.3Nov 20, 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
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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hypothetical protein TTHA0625
B: hypothetical protein TTHA0625
C: hypothetical protein TTHA0625
D: hypothetical protein TTHA0625


Theoretical massNumber of molelcules
Total (without water)113,2214
Polymers113,2214
Non-polymers00
Water7,746430
1
A: hypothetical protein TTHA0625
D: hypothetical protein TTHA0625


Theoretical massNumber of molelcules
Total (without water)56,6112
Polymers56,6112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3190 Å2
ΔGint-31 kcal/mol
Surface area18890 Å2
MethodPISA
2
B: hypothetical protein TTHA0625
C: hypothetical protein TTHA0625


Theoretical massNumber of molelcules
Total (without water)56,6112
Polymers56,6112
Non-polymers00
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area3140 Å2
ΔGint-29 kcal/mol
Surface area18900 Å2
MethodPISA
3
A: hypothetical protein TTHA0625
D: hypothetical protein TTHA0625

B: hypothetical protein TTHA0625
C: hypothetical protein TTHA0625


Theoretical massNumber of molelcules
Total (without water)113,2214
Polymers113,2214
Non-polymers00
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation3_655-y+1,x,z+1/41
Buried area9460 Å2
ΔGint-70 kcal/mol
Surface area34650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)76.481, 76.481, 193.940
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
hypothetical protein TTHA0625


Mass: 28305.311 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermus thermophilus (bacteria) / Strain: HB8 / Plasmid: pET11a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q5SKL8
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 430 / 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: 2.5 Å3/Da / Density % sol: 51.1 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.2
Details: magnesium chloride, Sodium Citrate, MPD, pH 6.2, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL26B1 / Wavelength: 0.9, 0.9791, 0.9795
DetectorType: RIGAKU JUPITER 210 / Detector: CCD / Date: Jul 2, 2004
RadiationMonochromator: SI 111 / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.91
20.97911
30.97951
ReflectionResolution: 2.501→20 Å / Num. all: 75502 / Num. obs: 75502 / % possible obs: 99.9 % / Redundancy: 3.2 % / Biso Wilson estimate: 32.6 Å2 / Rmerge(I) obs: 0.047 / Net I/σ(I): 33.1
Reflection shellResolution: 2.5→2.66 Å / Redundancy: 2.9 % / Rmerge(I) obs: 0.166 / Mean I/σ(I) obs: 9

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Processing

Software
NameVersionClassification
CNS1.1refinement
HKL-2000data reduction
SCALEPACKdata scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.5→19.78 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 249701.96 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.247 7316 9.9 %RANDOM
Rwork0.197 ---
all0.203 ---
obs0.197 74178 97.7 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 37.8364 Å2 / ksol: 0.371205 e/Å3
Displacement parametersBiso mean: 22.8 Å2
Baniso -1Baniso -2Baniso -3
1--1.83 Å20 Å20 Å2
2---2.66 Å20 Å2
3---4.49 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.27 Å
Luzzati d res low-5 Å
Luzzati sigma a0.35 Å0.25 Å
Refinement stepCycle: LAST / Resolution: 2.5→19.78 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7908 0 0 430 8338
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d25.7
X-RAY DIFFRACTIONc_improper_angle_d0.9
X-RAY DIFFRACTIONc_mcbond_it3.931.5
X-RAY DIFFRACTIONc_mcangle_it6.072
X-RAY DIFFRACTIONc_scbond_it7.132
X-RAY DIFFRACTIONc_scangle_it10.352.5
LS refinement shellResolution: 2.5→2.66 Å / Rfactor Rfree error: 0.009 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.299 1194 9.9 %
Rwork0.222 10887 -
obs--94.9 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1protein_rep.paramprotein.top
X-RAY DIFFRACTION2water_rep.paramwater_protin.top
X-RAY DIFFRACTION3ion.paramion.top

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