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- PDB-3r2j: Crystal Structure of PnC1 from L. infantum in complex with nicotinate -

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Basic information

Entry
Database: PDB / ID: 3r2j
TitleCrystal Structure of PnC1 from L. infantum in complex with nicotinate
ComponentsAlpha/beta-hydrolase-like protein
KeywordsHYDROLASE / alpha/beta-hydrolase-like / nicotinamidase / cytoplasmic
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
NICOTINIC ACID / Alpha/beta-hydrolase-like protein
Similarity search - Component
Biological speciesLeishmania infantum (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.68 Å
AuthorsGazanion, E. / Garcia, D. / Guichou, J.-F. / Labesse, G. / Sereno, D. / Vergnes, B.
CitationJournal: Mol.Microbiol. / Year: 2011
Title: The Leishmania nicotinamidase is essential for NAD(+) production and parasite proliferation.
Authors: Gazanion, E. / Garcia, D. / Silvestre, R. / Gerard, C. / Guichou, J.F. / Labesse, G. / Seveno, M. / Cordeiro-Da-Silva, A. / Ouaissi, A. / Sereno, D. / Vergnes, B.
History
DepositionMar 14, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 24, 2011Provider: repository / Type: Initial release
Revision 1.1Oct 12, 2011Group: Database references
Revision 1.2Sep 13, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_ref_seq_dif / 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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Alpha/beta-hydrolase-like protein
B: Alpha/beta-hydrolase-like protein
C: Alpha/beta-hydrolase-like protein
D: Alpha/beta-hydrolase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)97,01214
Polymers96,1874
Non-polymers82510
Water2,144119
1
A: Alpha/beta-hydrolase-like protein
B: Alpha/beta-hydrolase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5067
Polymers48,0942
Non-polymers4125
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-81 kcal/mol
Surface area15280 Å2
MethodPISA
2
C: Alpha/beta-hydrolase-like protein
D: Alpha/beta-hydrolase-like protein
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,5067
Polymers48,0942
Non-polymers4125
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2750 Å2
ΔGint-80 kcal/mol
Surface area15190 Å2
MethodPISA
Unit cell
Length a, b, c (Å)123.386, 123.386, 114.993
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number90
Space group name H-MP4212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Component-ID: 1 / Ens-ID: 1 / Beg auth comp-ID: CYS / Beg label comp-ID: CYS / End auth comp-ID: GLU / End label comp-ID: GLU / Refine code: 5 / Auth seq-ID: 18 - 214 / Label seq-ID: 27 - 223

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB
3CC
4DD

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Components

#1: Protein
Alpha/beta-hydrolase-like protein


Mass: 24046.830 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania infantum (eukaryote) / Gene: LinJ01.0460 / Plasmid: pET-45b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3) / References: UniProt: A4HRG8, nicotinamidase
#2: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Zn
#3: Chemical
ChemComp-NIO / NICOTINIC ACID


Mass: 123.109 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C6H5NO2
#4: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Cl
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / 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: 2.28 Å3/Da / Density % sol: 45.94 %
Crystal growTemperature: 291 K / Method: vapor diffusion, sitting drop / pH: 7.5
Details: 0.1M HEPES, 0.7 M NaCitrate, pH 7.5, VAPOR DIFFUSION, SITTING DROP, temperature 291K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.979138 Å
DetectorType: ADSC QUANTUM 315r / Detector: CCD / Date: Jun 11, 2010
RadiationMonochromator: Si 111 CHANNEL / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979138 Å / Relative weight: 1
ReflectionResolution: 2.64→123.37 Å / Num. all: 28874 / Num. obs: 28817 / % possible obs: 99.8 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Redundancy: 4.3 % / Rmerge(I) obs: 0.111 / Rsym value: 0.1 / Net I/σ(I): 96.3
Reflection shellResolution: 2.64→2.7 Å / Redundancy: 4.6 % / Mean I/σ(I) obs: 18.1 / Rsym value: 0.835 / % possible all: 99.9

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Processing

Software
NameVersionClassification
ADSCQuantumdata collection
MOLREPphasing
REFMAC5.5.0102refinement
MOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 3GBC

3gbc
PDB Unreleased entry


Resolution: 2.68→57.25 Å / Cor.coef. Fo:Fc: 0.929 / Cor.coef. Fo:Fc free: 0.878 / SU B: 37.438 / SU ML: 0.325 / Cross valid method: THROUGHOUT / ESU R Free: 0.411 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.29789 1272 5.1 %RANDOM
Rwork0.21355 ---
obs0.21775 23896 98.56 %-
all-24262 --
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: MASK
Displacement parametersBiso mean: 28.181 Å2
Baniso -1Baniso -2Baniso -3
1-0.03 Å20 Å20 Å2
2--0.03 Å20 Å2
3----0.06 Å2
Refinement stepCycle: LAST / Resolution: 2.68→57.25 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5899 0 42 119 6060
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0090.0216060
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.3041.9348257
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6855792
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.04524.104251
X-RAY DIFFRACTIONr_dihedral_angle_3_deg19.74515882
X-RAY DIFFRACTIONr_dihedral_angle_4_deg22.7751528
X-RAY DIFFRACTIONr_chiral_restr0.0870.2961
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0214632
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3071.53929
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.59226272
X-RAY DIFFRACTIONr_scbond_it0.89132131
X-RAY DIFFRACTIONr_scangle_it1.4494.51985
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Dom-ID: 1 / Ens-ID: 1 / Refine-ID: X-RAY DIFFRACTION

Auth asym-IDNumberTypeRms dev position (Å)Weight position
A788medium positional0.270.5
B788medium positional0.390.5
C788medium positional0.280.5
D788medium positional0.30.5
A667loose positional0.685
B667loose positional0.835
C667loose positional0.635
D667loose positional0.645
A788medium thermal0.312
B788medium thermal0.322
C788medium thermal0.282
D788medium thermal0.32
A667loose thermal0.4510
B667loose thermal0.4710
C667loose thermal0.4510
D667loose thermal0.4810
LS refinement shellResolution: 2.68→2.749 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.494 100 -
Rwork0.384 1672 -
obs--96.83 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.24281.14560.69254.14240.78293.38910.03810.2958-0.0809-0.50190.0417-0.26380.26280.2968-0.07980.110.04620.04910.04860.03340.084538.00612.51316.934
24.2942-0.21170.55862.534-0.34552.13210.1551-0.2409-0.01380.124-0.04760.30720.0448-0.2301-0.10760.1017-0.00020.0640.06120.02330.096923.9426.78539.014
32.72761.330.49193.4709-0.062.29860.00090.2153-0.0277-0.4949-0.038-0.21520.05730.25430.03710.10770.02570.01550.04640.02560.06599.76774.90719.873
42.7257-0.36710.85671.7532-0.12163.6175-0.0691-0.2831-0.01060.1272-0.00530.2448-0.0589-0.34760.07430.0571-0.02410.01680.0649-0.00140.093185.92469.80342.35
50.55540.94630.0220.6169-0.080.532-0.18780.02480.0659-0.2513-0.0258-0.06610.0173-0.12420.21370.19570.0051-0.08970.1779-0.00080.254570.62730.71553.528
60.06940.15650.04920.34270.0432-0.0934-0.056-0.03530.0403-0.06720.0290.04570.005-0.00090.0270.1654-0.0273-0.00560.0914-0.00880.12160.64241.15131.157
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A16 - 311
2X-RAY DIFFRACTION2B15 - 311
3X-RAY DIFFRACTION3C17 - 311
4X-RAY DIFFRACTION4D16 - 311
5X-RAY DIFFRACTION5B321
6X-RAY DIFFRACTION5D321
7X-RAY DIFFRACTION6A401 - 427
8X-RAY DIFFRACTION6B401 - 435
9X-RAY DIFFRACTION6C401 - 431
10X-RAY DIFFRACTION6D401 - 426

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