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- PDB-1kyt: Crystal Structure of Thermoplasma acidophilum 0175 (APC014) -

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Basic information

Entry
Database: PDB / ID: 1kyt
TitleCrystal Structure of Thermoplasma acidophilum 0175 (APC014)
Componentshypothetical protein TA0175
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / putative hydrolase / PSI / Protein Structure Initiative / Midwest Center for Structural Genomics / MCSG
Function / homology
Function and homology information


phosphoglycolate phosphatase / phosphoglycolate phosphatase activity / magnesium ion binding / cytosol
Similarity search - Function
Phosphoglycolate phosphatase / Hypothetical Protein Ta0175; Chain: A, domain 2 - #10 / Hypothetical Protein Ta0175; Chain: A, domain 2 / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Alpha-Beta Complex / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Phosphoglycolate phosphatase
Similarity search - Component
Biological speciesThermoplasma acidophilum (acidophilic)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.7 Å
AuthorsKim, Y. / Joachimiak, A. / Edwards, A. / Xu, X. / Pennycooke, M. / Gu, J. / Cheung, F. / Christendat, D. / Midwest Center for Structural Genomics (MCSG)
CitationJournal: To be published
Title: Crystal Structure of Thermoplasma acidophilum 0175 (APC014)
Authors: Kim, Y. / Joachimiak, A. / Edwards, A. / Xu, X. / Pennycooke, M. / Gu, J. / Cheung, F. / Christendat, D.
History
DepositionFeb 5, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 21, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Oct 11, 2017Group: Refinement description / Category: software
Revision 1.4Oct 27, 2021Group: Database references / Derived calculations
Category: database_2 / pdbx_struct_conn_angle ...database_2 / pdbx_struct_conn_angle / 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 / _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_atom_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.ptnr2_auth_asym_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr2_label_asym_id / _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_atom_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.conn_type_id / _struct_conn.id / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_ptnr1_label_alt_id / _struct_conn.pdbx_ptnr2_label_alt_id / _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 / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 300BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S) ...BIOMOLECULE: 1 THIS ENTRY CONTAINS THE CRYSTALLOGRAPHIC ASYMMETRIC UNIT WHICH CONSISTS OF 2 CHAIN(S). SEE REMARK 350 FOR INFORMATION ON GENERATING THE BIOLOGICAL MOLECULE(S). IT APPEARS THIS PROTEIN FORMS A DIMER, ALTHOUGH THERE IS NO HARD EVIDENCE EXCEPT FOR THE SIGNIFICANT INTERFACE.

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: hypothetical protein TA0175
B: hypothetical protein TA0175
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2918
Polymers52,0502
Non-polymers2406
Water7,873437
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
A: hypothetical protein TA0175
hetero molecules

B: hypothetical protein TA0175
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,2918
Polymers52,0502
Non-polymers2406
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation6_554-x+1/2,-y+1/2,z-1/21
Buried area3090 Å2
ΔGint-78 kcal/mol
Surface area18230 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.526, 99.316, 113.886
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number23
Space group name H-MI222

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Components

#1: Protein hypothetical protein TA0175


Mass: 26025.049 Da / Num. of mol.: 2 / Mutation: T12N
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermoplasma acidophilum (acidophilic) / Gene: TA0175 / Production host: Escherichia coli (E. coli) / References: UniProt: Q9HLQ2
#2: Chemical
ChemComp-CA / CALCIUM ION


Mass: 40.078 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: Ca
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 437 / 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

CrystalDensity Matthews: 2.4 Å3/Da / Density % sol: 48.84 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG 3350, sodium HEPES, Calcium Chloride, Glycerol, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K

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Data collection

Diffraction
IDMean temperature (K)Crystal-ID
11501
21501
1,21
Diffraction source
SourceSiteBeamlineIDWavelength (Å)
SYNCHROTRONAPS 19-ID11.0719
SYNCHROTRONAPS 19-BM20.96411, 0.97939, 0.9795
Detector
TypeIDDetectorDateDetails
SBC-21CCDNov 30, 2001mirror
SBC-12CCDNov 26, 2001mirror
Radiation
IDMonochromatorProtocolMonochromatic (M) / Laue (L)Scattering typeWavelength-ID
1double crystal monochromatorSINGLE WAVELENGTHMx-ray1
2SAGITALLY FOCUSED Si(111)MADMx-ray1
Radiation wavelength
IDWavelength (Å)Relative weight
11.07191
20.964111
30.979391
40.97951
ReflectionResolution: 1.7→43.14 Å / Num. all: 53243 / Num. obs: 53243 / % possible obs: 97.4 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 5.5 % / Biso Wilson estimate: 14.6 Å2 / Rmerge(I) obs: 0.074 / Net I/σ(I): 7.4
Reflection shellResolution: 1.7→1.76 Å / Redundancy: 2.1 % / Rmerge(I) obs: 0.244 / Mean I/σ(I) obs: 2.6 / Num. unique all: 4407 / % possible all: 81.6

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Processing

Software
NameVersionClassification
d*TREKdata scaling
HKL-2000data collection
SCALEPACKdata scaling
CNSrefinement
CrystalClearD*STREK (MSC/RIGAKU)data reduction
HKL-2000data reduction
CNSphasing
RefinementMethod to determine structure: MAD / Resolution: 1.7→43.14 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 331388.1 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: Engh & Huber
Details: The GLY and SER of the cloning artifact are disordered.
RfactorNum. reflection% reflectionSelection details
Rfree0.246 5224 10.1 %RANDOM
Rwork0.224 ---
all0.226 51727 --
obs0.226 51727 93.3 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 51.5452 Å2 / ksol: 0.399546 e/Å3
Displacement parametersBiso mean: 17.5 Å2
Baniso -1Baniso -2Baniso -3
1--1.85 Å20 Å20 Å2
2--7.89 Å20 Å2
3----6.04 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.25 Å0.23 Å
Luzzati d res low-5 Å
Luzzati sigma a0.22 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.7→43.14 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3576 0 6 437 4019
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.008
X-RAY DIFFRACTIONc_bond_d_na
X-RAY DIFFRACTIONc_bond_d_prot
X-RAY DIFFRACTIONc_angle_d
X-RAY DIFFRACTIONc_angle_d_na
X-RAY DIFFRACTIONc_angle_d_prot
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d23.4
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.88
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.651.5
X-RAY DIFFRACTIONc_mcangle_it2.22
X-RAY DIFFRACTIONc_scbond_it2.852
X-RAY DIFFRACTIONc_scangle_it4.052.5
LS refinement shellResolution: 1.7→1.81 Å / Rfactor Rfree error: 0.012 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.305 667 9.8 %
Rwork0.296 6162 -
obs--74.8 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMION.TOP
X-RAY DIFFRACTION3ION.PARAMWATER.TOP

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