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- PDB-1ydf: Crystal structure of a HAD-like phosphatase from Streptococcus pn... -

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Basic information

Entry
Database: PDB / ID: 1ydf
TitleCrystal structure of a HAD-like phosphatase from Streptococcus pneumoniae
Componentshydrolase, haloacid dehalogenase-like family
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / Protein structure initiative / Hypothetical protein / NYSGXRC / hydrolase haloacid dehalogenase-like family / PSI / New York SGX Research Center for Structural Genomics
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
HAD-superfamily hydrolase, subfamily IIA, hypothetical 1 / HAD-superfamily hydrolase, subfamily IIA / Haloacid dehalogenase-like hydrolase / HAD-hyrolase-like / HAD superfamily/HAD-like / HAD superfamily / HAD-like superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Hydrolase, haloacid dehalogenase-like family / Acid sugar phosphatase
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 2.6 Å
AuthorsSeetharaman, J. / Swaminathan, S. / Burley, S.K. / New York SGX Research Center for Structural Genomics (NYSGXRC)
CitationJournal: To be Published
Title: Crystal Structure of a Hypothetical protein, hydrolase haloacid dehalogenase-like family
Authors: Seetharaman, J. / Swaminathan, S.
History
DepositionDec 23, 2004Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 18, 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 1.3Feb 3, 2021Group: Database references / Derived calculations / Structure summary
Category: audit_author / pdbx_struct_conn_angle ...audit_author / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _audit_author.identifier_ORCID / _pdbx_struct_conn_angle.ptnr1_auth_comp_id ..._audit_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.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_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Feb 14, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: hydrolase, haloacid dehalogenase-like family
hetero molecules


Theoretical massNumber of molelcules
Total (without water)28,2142
Polymers28,1901
Non-polymers241
Water1,54986
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)74.430, 99.929, 39.841
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212

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Components

#1: Protein hydrolase, haloacid dehalogenase-like family


Mass: 28190.059 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97Q24, UniProt: A0A0H2UQJ9*PLUS
#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.: 86 / 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: 1

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Sample preparation

CrystalDensity Matthews: 2.5 Å3/Da / Density % sol: 51 %
Crystal growTemperature: 293 K / pH: 8.5
Details: MgCl2, Tris HCL, PEG3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K, pH 8.50

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X29A / Wavelength: 0.9790, 0.97938, 0.95
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Nov 2, 2004
RadiationMonochromator: MIRRORS / Protocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.9791
20.979381
30.951
ReflectionResolution: 2.6→50 Å / Num. obs: 11211 / % possible obs: 97.5 % / Observed criterion σ(I): 0 / Redundancy: 12.19 % / Biso Wilson estimate: 49.3 Å2 / Rsym value: 0.084 / Net I/σ(I): 13.4
Reflection shellResolution: 2.6→2.7 Å / Redundancy: 8.3 % / Rmerge(I) obs: 0.33 / Mean I/σ(I) obs: 11 / % possible all: 86

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Processing

Software
NameVersionClassification
CNS1.1refinement
CBASSdata collection
HKL-2000data scaling
SOLVEphasing
RefinementMethod to determine structure: MAD / Resolution: 2.6→41.49 Å / Rfactor Rfree error: 0.009 / Data cutoff high absF: 198655.04 / Data cutoff low absF: 0 / Isotropic thermal model: RESTRAINED / Cross valid method: THROUGHOUT / σ(F): 0 / Stereochemistry target values: ENGH & HUBER
Details: the electron density for the side chain atoms listed in remark 470 was weak.
RfactorNum. reflection% reflectionSelection details
Rfree0.267 925 10 %RANDOM
Rwork0.217 ---
obs0.217 9234 95.6 %-
all-11211 --
Solvent computationSolvent model: FLAT MODEL / Bsol: 44.72 Å2 / ksol: 0.39 e/Å3
Displacement parametersBiso mean: 39.4 Å2
Baniso -1Baniso -2Baniso -3
1--1.97 Å20 Å20 Å2
2---12.92 Å20 Å2
3---14.89 Å2
Refine analyze
FreeObs
Luzzati coordinate error0.43 Å0.33 Å
Luzzati d res low-5 Å
Luzzati sigma a0.46 Å0.37 Å
Refinement stepCycle: LAST / Resolution: 2.6→41.49 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1952 0 1 86 2039
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONc_bond_d0.007
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_deg1.3
X-RAY DIFFRACTIONc_angle_deg_na
X-RAY DIFFRACTIONc_angle_deg_prot
X-RAY DIFFRACTIONc_dihedral_angle_d
X-RAY DIFFRACTIONc_dihedral_angle_d_na
X-RAY DIFFRACTIONc_dihedral_angle_d_prot
X-RAY DIFFRACTIONc_improper_angle_d0.81
X-RAY DIFFRACTIONc_improper_angle_d_na
X-RAY DIFFRACTIONc_improper_angle_d_prot
X-RAY DIFFRACTIONc_mcbond_it1.171.5
X-RAY DIFFRACTIONc_mcangle_it1.932
X-RAY DIFFRACTIONc_scbond_it1.82
X-RAY DIFFRACTIONc_scangle_it2.732.5
LS refinement shellResolution: 2.6→2.76 Å / Rfactor Rfree error: 0.032 / Total num. of bins used: 6
RfactorNum. reflection% reflection
Rfree0.343 114 8.8 %
Rwork0.305 1179 -
obs--82.3 %
Xplor file
Refine-IDSerial noParam fileTopol file
X-RAY DIFFRACTION1PROTEIN_REP.PARAMTOPOLOGY.INFILE.1.TOP
X-RAY DIFFRACTION2WATER_REP.PARAMTOPOLOGY.INFILE.2.TOP
X-RAY DIFFRACTION3ION.PARAMTOPOLOGY.INFILE.3.TOP
X-RAY DIFFRACTION4TOPOLOGY.INFILE.4.TOP
X-RAY DIFFRACTION5TOPOLOGY.INFILE.5.TOP

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