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- PDB-3mc1: Crystal structure of a predicted phosphatase from Clostridium ace... -

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Basic information

Entry
Database: PDB / ID: 3mc1
TitleCrystal structure of a predicted phosphatase from Clostridium acetobutylicum
ComponentsPredicted phosphatase, HAD family
KeywordsHYDROLASE / PSI2 / NYSGXRC / Structural Genomics / Protein Structure Initiative / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


protein tyrosine kinase activity / cytosol
Similarity search - Function
: / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold ...: / Haloacid dehalogenase-like hydrolase / Haloacid dehalogenase-like hydrolase / Putative phosphatase; domain 2 / Phosphoglycolate phosphatase-like, domain 2 / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / DNA polymerase; domain 1 / Rossmann fold / Orthogonal Bundle / 3-Layer(aba) Sandwich / Mainly Alpha / Alpha Beta
Similarity search - Domain/homology
Predicted phosphatase, HAD family
Similarity search - Component
Biological speciesClostridium acetobutylicum (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.93 Å
AuthorsEswaramoorthy, S. / Burley, S.K. / Swaminathan, S. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published / Year: 2010
Title: Crystal structure of a predicted phosphatase from Clostridium acetobutylicum
Authors: Eswaramoorthy, S. / Burley, S.K. / Swaminathan, S.
History
DepositionMar 26, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 7, 2010Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 10, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / citation_author ...audit_author / citation_author / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _audit_author.identifier_ORCID / _citation_author.identifier_ORCID ..._audit_author.identifier_ORCID / _citation_author.identifier_ORCID / _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.pdbx_leaving_atom_flag / _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.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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Oct 16, 2024Group: Data collection / Database references / Structure summary
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_entry_details / pdbx_modification_feature
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Predicted phosphatase, HAD family
B: Predicted phosphatase, HAD family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1328
Polymers51,8312
Non-polymers3016
Water1,856103
1
A: Predicted phosphatase, HAD family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0664
Polymers25,9151
Non-polymers1513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Predicted phosphatase, HAD family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)26,0664
Polymers25,9151
Non-polymers1513
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
A: Predicted phosphatase, HAD family
hetero molecules

B: Predicted phosphatase, HAD family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,1328
Polymers51,8312
Non-polymers3016
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation1_655x+1,y,z1
Buried area2650 Å2
ΔGint-58 kcal/mol
Surface area17650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)63.938, 53.524, 64.182
Angle α, β, γ (deg.)90.00, 97.10, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein Predicted phosphatase, HAD family


Mass: 25915.408 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Details: BL21(DE3)-Codon+RIL(p) - Stratagene / Source: (gene. exp.) Clostridium acetobutylicum (bacteria) / Gene: CA_C0418 / Plasmid: BC-pSGX3 (BC) / Production host: Escherichia coli (E. coli) / References: UniProt: Q97LY2
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 103 / 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: 2.1 Å3/Da / Density % sol: 41.5 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 5.5
Details: 25% PEG 3350; 0.1M BisTris pH 5.5; 0.2M NaCl and Dimethyl sulfoxide, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X12C / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 21, 2010 / Details: mirrors
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 1.93→50 Å / Num. all: 32453 / Num. obs: 32453 / % possible obs: 99 % / Observed criterion σ(F): 0 / Observed criterion σ(I): -3 / Redundancy: 7.4 % / Biso Wilson estimate: 21 Å2 / Rmerge(I) obs: 0.075 / Rsym value: 0.075 / Net I/σ(I): 13.8
Reflection shellResolution: 1.93→2 Å / Redundancy: 6.7 % / Rmerge(I) obs: 0.306 / Mean I/σ(I) obs: 5.9 / Num. unique all: 2922 / Rsym value: 0.306 / % possible all: 89.9

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Processing

Software
NameVersionClassification
CBASSdata collection
SHELXmodel building
SHARPphasing
CNS1.1refinement
HKL-2000data reduction
HKL-2000data scaling
SHELXphasing
RefinementMethod to determine structure: SAD / Resolution: 1.93→50 Å / Cross valid method: THROUGHOUT / σ(F): 0 / σ(I): 0 / Stereochemistry target values: Engh & Huber
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1280 -RANDOM
Rwork0.224 ---
all0.245 31810 --
obs0.245 31810 97.6 %-
Displacement parametersBiso mean: 24.9 Å2
Baniso -1Baniso -2Baniso -3
1--2.38 Å20 Å21.72 Å2
2--2.76 Å20 Å2
3----0.38 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.33 Å0.25 Å
Luzzati d res low-5 Å
Luzzati sigma a0.29 Å0.21 Å
Refinement stepCycle: LAST / Resolution: 1.93→50 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3430 0 16 103 3549
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONc_bond_d0.006
X-RAY DIFFRACTIONc_angle_deg1.3
X-RAY DIFFRACTIONc_dihedral_angle_deg21.7
X-RAY DIFFRACTIONc_improper_angle_deg0.69
LS refinement shellResolution: 1.93→2.05 Å / Rfactor Rfree error: 0.025
RfactorNum. reflection% reflection
Rfree0.358 203 -
Rwork0.278 --
obs-4761 92.2 %

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