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- PDB-3o90: High resolution crystal structures of Streptococcus pneumoniae ni... -

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Basic information

Entry
Database: PDB / ID: 3o90
TitleHigh resolution crystal structures of Streptococcus pneumoniae nicotinamidase with trapped intermediates provide insights into catalytic mechanism and inhibition by aldehydes
Componentsnicotinamidase
KeywordsHYDROLASE / Nicotinamidase
Function / homology
Function and homology information


hydrolase activity / metal ion binding
Similarity search - Function
Isochorismatase-like / Isochorismatase-like / Isochorismatase-like superfamily / Isochorismatase family / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Isochorismatase family protein / Isochorismatase family protein
Similarity search - Component
Biological speciesStreptococcus pneumoniae (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.94 Å
AuthorsFrench, J.B. / Cen, Y. / Sauve, A.A. / Ealick, S.E.
CitationJournal: Biochemistry / Year: 2010
Title: High-resolution crystal structures of Streptococcus pneumoniae nicotinamidase with trapped intermediates provide insights into the catalytic mechanism and inhibition by aldehydes .
Authors: French, J.B. / Cen, Y. / Sauve, A.A. / Ealick, S.E.
History
DepositionAug 3, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 12, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Feb 21, 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_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.ptnr2_auth_asym_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.value / _struct_conn.pdbx_dist_value / _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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: nicotinamidase
B: nicotinamidase
C: nicotinamidase
D: nicotinamidase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)94,7638
Polymers94,5024
Non-polymers2624
Water9,584532
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7590 Å2
ΔGint-171 kcal/mol
Surface area28020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.838, 120.875, 63.180
Angle α, β, γ (deg.)90.00, 114.31, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
nicotinamidase / / Isochorismatase family protein


Mass: 23625.445 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Streptococcus pneumoniae (bacteria) / Strain: TIGR4 / Gene: SP_1583 / Production host: Escherichia coli (E. coli) / References: UniProt: Q97PM2, UniProt: A0A0H2UR34*PLUS
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 532 / 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: 2.24 Å3/Da / Density % sol: 45.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion, hanging drop / pH: 6.3
Details: 18-22% PEG 3350, 0.2-0.3M NaCl, 0.2M Sodium Malonate, pH 6.3, VAPOR DIFFUSION, HANGING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9795 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Aug 15, 2008
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9795 Å / Relative weight: 1
ReflectionResolution: 1.94→50 Å / Num. obs: 54000 / % possible obs: 88.2 % / Observed criterion σ(I): 2 / Redundancy: 3.4 % / Rsym value: 0.132 / Net I/σ(I): 11.3
Reflection shellResolution: 1.92→1.95 Å / Redundancy: 2.1 % / Mean I/σ(I) obs: 2.2 / Rsym value: 0.292 / % possible all: 73.7

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0109refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.94→41.7 Å / Cor.coef. Fo:Fc: 0.931 / Cor.coef. Fo:Fc free: 0.9 / SU B: 3.906 / SU ML: 0.115 / Cross valid method: THROUGHOUT / ESU R Free: 0.19 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.26077 2719 5 %RANDOM
Rwork0.21812 ---
obs0.22025 51165 87.03 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 24.99 Å2
Baniso -1Baniso -2Baniso -3
1-0.11 Å20 Å20.21 Å2
2---0.04 Å20 Å2
3---0.11 Å2
Refinement stepCycle: LAST / Resolution: 1.94→41.7 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5792 0 4 532 6328
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0060.0215988
X-RAY DIFFRACTIONr_angle_refined_deg0.9231.9388139
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.8725746
X-RAY DIFFRACTIONr_dihedral_angle_2_deg28.33723.172290
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.73715935
X-RAY DIFFRACTIONr_dihedral_angle_4_deg16.721542
X-RAY DIFFRACTIONr_chiral_restr0.0640.2909
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0214621
X-RAY DIFFRACTIONr_mcbond_it0.3461.53687
X-RAY DIFFRACTIONr_mcangle_it0.66425917
X-RAY DIFFRACTIONr_scbond_it0.83332301
X-RAY DIFFRACTIONr_scangle_it1.4024.52215
LS refinement shellResolution: 1.935→1.986 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.316 157 -
Rwork0.246 2748 -
obs--63.64 %

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