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- PDB-2cs7: 1.2 A Crystal structure of the S. pneumoniae PhtA histidine triad... -

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Basic information

Entry
Database: PDB / ID: 2cs7
Title1.2 A Crystal structure of the S. pneumoniae PhtA histidine triad domain a novel zinc binding fold
Componentspneumococcal histidine triad A protein
KeywordsSTRUCTURAL GENOMICS / UNKNOWN FUNCTION / PhtA / Pneumococcal Histidine Triad Protein / S.pneumoniae
Function / homology
Function and homology information


Chitinase A; domain 3 - #90 / Streptococcal histidine triad repeat / Histidine triad protein / PhtA domain superfamily / Streptococcal histidine triad protein / Chitinase A; domain 3 / Roll / Alpha Beta
Similarity search - Domain/homology
: / Conserved domain protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / SAD / Resolution: 1.2 Å
AuthorsRiboldi-Tunnicliffe, A. / Isaacs, N.W. / Mitchell, T.J.
CitationJournal: Febs Lett. / Year: 2005
Title: 1.2 Angstroms crystal structure of the S. pneumoniae PhtA histidine triad domain a novel zinc binding fold.
Authors: Riboldi-Tunnicliffe, A. / Isaacs, N.W. / Mitchell, T.J.
History
DepositionMay 20, 2005Deposition site: PDBJ / Processing site: RCSB
Revision 1.0Feb 14, 2006Provider: repository / Type: Initial release
Revision 1.1Apr 30, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Feb 14, 2024Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / 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_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_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: pneumococcal histidine triad A protein
B: pneumococcal histidine triad A protein
C: pneumococcal histidine triad A protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)18,2726
Polymers18,0763
Non-polymers1963
Water3,513195
1
A: pneumococcal histidine triad A protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0912
Polymers6,0251
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: pneumococcal histidine triad A protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0912
Polymers6,0251
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: pneumococcal histidine triad A protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)6,0912
Polymers6,0251
Non-polymers651
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)62.182, 35.895, 72.541
Angle α, β, γ (deg.)90.00, 90.01, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11B-237-

HOH

21C-242-

HOH

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Components

#1: Protein pneumococcal histidine triad A protein


Mass: 6025.408 Da / Num. of mol.: 3
Fragment: Pneumococcal Histidine Triad Protein Domain (residues 166-220)
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Gene: PhtA (18-220) / Plasmid: pQE10 / Production host: Escherichia coli (E. coli) / References: GenBank: 14972655, UniProt: A0A0H2UQ89*PLUS
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 195 / 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: 1.8 Å3/Da / Density % sol: 33 %
Crystal growTemperature: 290 K / Method: vapor diffusion, sitting drop / pH: 7
Details: 1.6M Ammonium Sulphate, 100mM Hepes, pH 7.0, VAPOR DIFFUSION, SITTING DROP, temperature 290K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ELETTRA / Beamline: 5.2R / Wavelength: 1 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: Aug 28, 2003 / Details: Mirrors
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.2→72.5 Å / Num. obs: 49793 / % possible obs: 93.9 % / Observed criterion σ(F): 2 / Observed criterion σ(I): 2

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Processing

Software
NameVersionClassification
REFMAC5.1.9999refinement
MOSFLMdata reduction
CCP4(SCALA)data scaling
SHARPphasing
RefinementMethod to determine structure: SAD / Resolution: 1.2→72.55 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.973 / SU B: 0.669 / SU ML: 0.014 / Cross valid method: THROUGHOUT / σ(F): 2 / ESU R: 0.031 / ESU R Free: 0.031 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.13498 2392 5.1 %RANDOM
Rwork0.11224 ---
all0.11341 ---
obs0.11341 44267 93.73 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 8.828 Å2
Baniso -1Baniso -2Baniso -3
1--0.04 Å20 Å20.04 Å2
2---0.01 Å20 Å2
3---0.06 Å2
Refinement stepCycle: LAST / Resolution: 1.2→72.55 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1295 0 3 195 1493
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0211328
X-RAY DIFFRACTIONr_bond_other_d0.0010.021098
X-RAY DIFFRACTIONr_angle_refined_deg1.931.9231807
X-RAY DIFFRACTIONr_angle_other_deg3.65432575
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.8955161
X-RAY DIFFRACTIONr_dihedral_angle_2_deg29.11325.275
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.32915189
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.333153
X-RAY DIFFRACTIONr_chiral_restr0.2350.2189
X-RAY DIFFRACTIONr_gen_planes_refined0.0110.021532
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02275
X-RAY DIFFRACTIONr_nbd_refined0.2180.2274
X-RAY DIFFRACTIONr_nbd_other0.1630.21088
X-RAY DIFFRACTIONr_nbtor_other0.1280.2695
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1710.2138
X-RAY DIFFRACTIONr_metal_ion_refined0.0420.212
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2530.212
X-RAY DIFFRACTIONr_symmetry_vdw_other0.3290.259
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.2440.215
X-RAY DIFFRACTIONr_mcbond_it1.9491.51067
X-RAY DIFFRACTIONr_mcbond_other0.91.5343
X-RAY DIFFRACTIONr_mcangle_it2.2921298
X-RAY DIFFRACTIONr_scbond_it3.2853673
X-RAY DIFFRACTIONr_scangle_it3.9064.5509
LS refinement shellResolution: 1.2→1.235 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.193 151
Rwork0.15 3090
Refinement TLS params.Method: refined / Origin x: 22.111 Å / Origin y: 9.181 Å / Origin z: 19.185 Å
111213212223313233
T-0.002 Å2-0.0002 Å20 Å2--0.0016 Å2-0.0002 Å2--0.0014 Å2
L0.0044 °2-0.0042 °2-0.0126 °2-0.0239 °20.0076 °2--0.0375 °2
S0.0005 Å °-0.0008 Å °-0.0016 Å °0.0003 Å °0.0016 Å °0.003 Å °-0.001 Å °0.0025 Å °-0.0021 Å °
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
1X-RAY DIFFRACTION1AA1 - 542 - 55
2X-RAY DIFFRACTION1BB1 - 542 - 55
3X-RAY DIFFRACTION1CC1 - 542 - 55

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