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- PDB-1nf2: X-ray crystal structure of TM0651 from Thermotoga maritima -

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Basic information

Entry
Database: PDB / ID: 1nf2
TitleX-ray crystal structure of TM0651 from Thermotoga maritima
Componentsphosphatase
KeywordsStructural genomics/Unknown function / Thermotoga maritima / Structural proteomics / phosphatase / HAD family / New fold / Structural genomics / BSGC structure funded by NIH / Protein Structure Initiative / PSI / Berkeley Structural Genomics Center / Structural genomics-Unknown function COMPLEX
Function / homology
Function and homology information


phosphatase activity / magnesium ion binding / cytosol
Similarity search - Function
Hypothetical cof family signature 1. / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 - #10 / Cof family / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold ...Hypothetical cof family signature 1. / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 - #10 / Cof family / Hypothetical Protein, Haloacid Dehalogenase-like Hydrolase; Chain: A; domain 2 / HAD-superfamily hydrolase, subfamily IIB / haloacid dehalogenase-like hydrolase / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Uncharacterized protein
Similarity search - Component
Biological speciesThermotoga maritima (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 2.2 Å
AuthorsShin, D.H. / Berkeley Structural Genomics Center (BSGC)
CitationJournal: Protein Sci. / Year: 2003
Title: Crystal structure of a phosphatase with a unique substrate binding domain from Thermotoga maritima
Authors: Shin, D.H. / Roberts, A. / Jancarik, J. / Yokota, H. / Kim, R. / Wemmer, D.E. / Kim, S.H.
History
DepositionDec 12, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Sep 16, 2003Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Nov 13, 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 / pdbx_struct_conn_angle / struct_conn / 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_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.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.value / _struct_conn.pdbx_dist_value / _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.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_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: phosphatase
B: phosphatase
C: phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,33212
Polymers93,6833
Non-polymers6499
Water8,899494
1
A: phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4444
Polymers31,2281
Non-polymers2163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
2
B: phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4444
Polymers31,2281
Non-polymers2163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
3
C: phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)31,4444
Polymers31,2281
Non-polymers2163
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPQS
4
C: phosphatase
hetero molecules

C: phosphatase
hetero molecules

A: phosphatase
B: phosphatase
hetero molecules

A: phosphatase
B: phosphatase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)188,66524
Polymers187,3666
Non-polymers1,29918
Water1086
TypeNameSymmetry operationNumber
crystal symmetry operation3_545x+1/2,y-1/2,z1
crystal symmetry operation4_646-x+3/2,y-1/2,-z+11
identity operation1_555x,y,z1
crystal symmetry operation2_756-x+2,y,-z+11
Buried area11300 Å2
ΔGint-278 kcal/mol
Surface area69310 Å2
MethodPISA
Unit cell
Length a, b, c (Å)158.410, 93.880, 98.420
Angle α, β, γ (deg.)90.00, 127.91, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein phosphatase


Mass: 31227.719 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Thermotoga maritima (bacteria) / Production host: Escherichia coli (E. coli) / References: UniProt: Q9WZB9
#2: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: SO4
#3: Chemical ChemComp-MG / MAGNESIUM ION


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


Mass: 18.015 Da / Num. of mol.: 494 / 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: 2.91 Å3/Da / Density % sol: 57.41 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 5.5
Details: AMS, pH 5.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K
Crystal grow
*PLUS
Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetailsChemical formula
1108 mg/mlprotein1drop
250 mMTris-HCl1droppH6.8
3220 mM1dropNaCl
45 mMdithiothreitol1drop
51.0 Mammonium sulfate1drop
60.1 Mcitric acid1droppH5.5
71.0 Mammonium sulfate1reservoir
80.1 Mcitric acid1reservoirpH5.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.1 / Wavelength: 1 Å
DetectorType: ADSC QUANTUM 4 / Detector: CCD / Date: Jun 23, 2001
RadiationMonochromator: Double crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→83.3 Å / Num. obs: 57785 / % possible obs: 99.8 % / Observed criterion σ(I): -3 / Redundancy: 3.7 % / Biso Wilson estimate: 15.3 Å2 / Rsym value: 0.096 / Net I/σ(I): 15.3
Reflection shellResolution: 2.2→2.24 Å / Redundancy: 3.5 % / Mean I/σ(I) obs: 3.2 / Num. unique all: 2866 / Rsym value: 0.353 / % possible all: 99.7
Reflection
*PLUS
Rmerge(I) obs: 0.096
Reflection shell
*PLUS
% possible obs: 99.7 % / Num. unique obs: 2866 / Rmerge(I) obs: 0.353

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Processing

Software
NameVersionClassification
DENZOdata reduction
SCALEPACKdata scaling
SOLVEphasing
CNS1refinement
RefinementMethod to determine structure: SAD / Resolution: 2.2→19.95 Å / Rfactor Rfree error: 0.003 / Data cutoff high absF: 185871.23 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0
RfactorNum. reflection% reflectionSelection details
Rfree0.263 5709 10.2 %RANDOM
Rwork0.217 ---
all0.2216 57785 --
obs0.217 56114 97.2 %-
Solvent computationSolvent model: FLAT MODEL / Bsol: 55.9322 Å2 / ksol: 0.35902 e/Å3
Displacement parametersBiso mean: 36.8 Å2
Baniso -1Baniso -2Baniso -3
1-0.82 Å20 Å23.41 Å2
2---0.02 Å20 Å2
3----0.8 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.35 Å0.28 Å
Luzzati d res low-5 Å
Luzzati sigma a0.33 Å0.26 Å
Refinement stepCycle: LAST / Resolution: 2.2→19.95 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6558 0 33 494 7085
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.012
X-RAY DIFFRACTIONc_angle_deg1.4
X-RAY DIFFRACTIONc_dihedral_angle_d23.2
X-RAY DIFFRACTIONc_improper_angle_d0.74
LS refinement shellResolution: 2.2→2.34 Å / Rfactor Rfree error: 0.011 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.339 886 9.9 %
Rwork0.282 8086 -
obs--94.1 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTIONA1PROTEIN_REP.PARAMPROTEIN.TOP
X-RAY DIFFRACTIONA2WATER_REP.PARAM
X-RAY DIFFRACTIONA3ION.PARAM
Refinement
*PLUS
Highest resolution: 2.2 Å / Lowest resolution: 20 Å
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_angle_deg1.36
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_deg23.22
X-RAY DIFFRACTIONc_improper_angle_d
X-RAY DIFFRACTIONc_improper_angle_deg0.74

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