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- PDB-3ndr: Crystal structure of tetrameric pyridoxal 4-dehydrogenase from Me... -

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Basic information

Entry
Database: PDB / ID: 3ndr
TitleCrystal structure of tetrameric pyridoxal 4-dehydrogenase from Mesorhizobium loti
Components3-oxoacyl-(Acyl-carrier protein) reductase
KeywordsOXIDOREDUCTASE / PYRIDOXAL / tPLDH / 4-PYRIDOXOLACTONE / SHORT CHAIN DEHYDROGENASE/REDUCTASE
Function / homology
Function and homology information


pyridoxal 4-dehydrogenase / pyridoxal 4-dehydrogenase activity / vitamin B6 catabolic process
Similarity search - Function
Short-chain dehydrogenase/reductase, conserved site / Short-chain dehydrogenases/reductases family signature. / Enoyl-(Acyl carrier protein) reductase / Short-chain dehydrogenase/reductase SDR / NAD(P)-binding Rossmann-like Domain / NAD(P)-binding domain superfamily / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Pyridoxal 4-dehydrogenase
Similarity search - Component
Biological speciesMesorhizobium loti (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.88 Å
AuthorsChu, H.N.
Citation
Journal: To be Published
Title: Crystal structure of tetrameric pyridoxal 4-dehydrogenase from Mesorhizobium loti
Authors: Chu, H.N. / Kobayashi, J. / Yoshikane, Y. / Mikami, B. / Yagi, T.
#1: Journal: Acta Crystallogr.,Sect.F / Year: 2010
Title: Crystallization and preliminary X-ray analysis of SDR-type pyridoxal dehydrogenase from Mesorhizobium loti
Authors: Chu, H.N. / Kobayashi, J. / Yoshikane, Y. / Mikami, B. / Yagi, T.
History
DepositionJun 8, 2010Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Jun 8, 2011Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Version format compliance
Revision 1.2Nov 1, 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 / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.3Nov 22, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2
Revision 1.4Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 3-oxoacyl-(Acyl-carrier protein) reductase
B: 3-oxoacyl-(Acyl-carrier protein) reductase
C: 3-oxoacyl-(Acyl-carrier protein) reductase
D: 3-oxoacyl-(Acyl-carrier protein) reductase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,2998
Polymers102,6464
Non-polymers2,6544
Water1,08160
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area14330 Å2
ΔGint-67 kcal/mol
Surface area29690 Å2
MethodPISA
Unit cell
Length a, b, c (Å)86.203, 51.109, 91.732
Angle α, β, γ (deg.)90.00, 89.36, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
31C
41D

NCS domain segments:

Ens-ID: 1

Dom-IDComponent-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDSelection detailsAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
11GLUGLUSERSERchain A and (resseq 3:50 or resseq 54:188 or resseq 197:248 )AA3 - 502 - 49
12LYSLYSGLUGLUchain A and (resseq 3:50 or resseq 54:188 or resseq 197:248 )AA54 - 18853 - 187
13HISHISHISHISchain A and (resseq 3:50 or resseq 54:188 or resseq 197:248 )AA197 - 248196 - 247
21GLUGLUSERSERchain B and (resseq 3:50 or resseq 54:188 or resseq 197:248 )BB3 - 502 - 49
22LYSLYSGLUGLUchain B and (resseq 3:50 or resseq 54:188 or resseq 197:248 )BB54 - 18853 - 187
23HISHISHISHISchain B and (resseq 3:50 or resseq 54:188 or resseq 197:248 )BB197 - 248196 - 247
31GLUGLUSERSERchain C and (resseq 3:50 or resseq 54:188 or resseq 197:248 )CC3 - 502 - 49
32LYSLYSGLUGLUchain C and (resseq 3:50 or resseq 54:188 or resseq 197:248 )CC54 - 18853 - 187
33HISHISHISHISchain C and (resseq 3:50 or resseq 54:188 or resseq 197:248 )CC197 - 248196 - 247
41GLUGLUSERSERchain D and (resseq 3:50 or resseq 54:188 or resseq 197:248 )DD3 - 502 - 49
42LYSLYSGLUGLUchain D and (resseq 3:50 or resseq 54:188 or resseq 197:248 )DD54 - 18853 - 187
43HISHISHISHISchain D and (resseq 3:50 or resseq 54:188 or resseq 197:248 )DD197 - 248196 - 247

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Components

#1: Protein
3-oxoacyl-(Acyl-carrier protein) reductase / Pyridoxal 4-dehydrogenase


Mass: 25661.389 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Mesorhizobium loti (bacteria) / Gene: mlr6807, pldh-t / Plasmid: Pet21a / Production host: Escherichia coli (E. coli) / Strain (production host): B834(DE3) / References: UniProt: Q988B7, pyridoxal 4-dehydrogenase
#2: Chemical
ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 60 / 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: 1.97 Å3/Da / Density % sol: 37.52 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.1M Sodium acetate, 0.1M Tris-HCl, 30% PEG4000, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 293.0K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SPring-8 / Beamline: BL38B1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Feb 1, 2010
RadiationMonochromator: DOUBLE-CRYSTAL MONOCHROMATOR / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.88→50 Å / Num. obs: 16995 / % possible obs: 97.4 % / Redundancy: 2.1 % / Biso Wilson estimate: 16.8 Å2 / Rmerge(I) obs: 0.108 / Net I/σ(I): 9.9
Reflection shellResolution: 2.88→3 Å / Redundancy: 1.9 % / Rmerge(I) obs: 0.43 / Mean I/σ(I) obs: 2.5 / Num. unique all: 3280 / % possible all: 97.1

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Processing

Software
NameVersionClassification
HKL-2000data collection
PHENIX(phenix.refine: 1.5_2)refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2EW8

2ew8


Resolution: 2.88→39.733 Å / Occupancy max: 1 / Occupancy min: 1 / SU ML: 0.33 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.248 916 5.12 %RANDOM
Rwork0.1848 ---
obs0.188 16988 97.09 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 14.068 Å2 / ksol: 0.314 e/Å3
Displacement parametersBiso max: 91.88 Å2 / Biso mean: 27.5892 Å2 / Biso min: 9.17 Å2
Baniso -1Baniso -2Baniso -3
1-4.8938 Å2-0 Å210.4744 Å2
2---3.5057 Å20 Å2
3----1.3882 Å2
Refinement stepCycle: LAST / Resolution: 2.88→39.733 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7148 0 176 60 7384
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0097444
X-RAY DIFFRACTIONf_angle_d1.17310132
X-RAY DIFFRACTIONf_dihedral_angle_d20.9132612
X-RAY DIFFRACTIONf_chiral_restr0.0751204
X-RAY DIFFRACTIONf_plane_restr0.0031292
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDNumberRefine-IDTypeRms dev position (Å)
11A1707X-RAY DIFFRACTIONPOSITIONAL0.05
12B1707X-RAY DIFFRACTIONPOSITIONAL0.05
13C1707X-RAY DIFFRACTIONPOSITIONAL0.053
14D1707X-RAY DIFFRACTIONPOSITIONAL0.051
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 7

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkNum. reflection all% reflection obs (%)
2.8804-3.03220.32351280.24032355248395
3.0322-3.22210.32641260.22692361248796
3.2221-3.47080.28561280.21272361248995
3.4708-3.81980.24141430.17082366250996
3.8198-4.37190.20431240.15272466259098
4.3719-5.50590.19771390.156524922631100
5.5059-39.73630.23461280.184225872715100

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