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- PDB-1qj3: Crystal structure of 7,8-diaminopelargonic acid synthase in compl... -

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Basic information

Entry
Database: PDB / ID: 1qj3
TitleCrystal structure of 7,8-diaminopelargonic acid synthase in complex with 7-keto-8-aminopelargonic acid
Components7,8-DIAMINOPELARGONIC ACID SYNTHASE
KeywordsTRANSFERASE / AMINOTRANSFERASE / PYRIDOXAL-5'-PHOSPHATE / BIOTIN BIOSYNTHESIS
Function / homology
Function and homology information


adenosylmethionine-8-amino-7-oxononanoate transaminase / adenosylmethionine-8-amino-7-oxononanoate transaminase activity / dethiobiotin synthase activity / biotin biosynthetic process / pyridoxal phosphate binding / protein homodimerization activity / cytoplasm
Similarity search - Function
Adenosylmethionine--8-amino-7-oxononanoate aminotransferase BioA / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain ...Adenosylmethionine--8-amino-7-oxononanoate aminotransferase BioA / : / Aminotransferases class-III pyridoxal-phosphate attachment site. / Aminotransferase class-III / Aminotransferase class-III / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase, domain 1 / Aspartate Aminotransferase; domain 2 / Type I PLP-dependent aspartate aminotransferase-like (Major domain) / Pyridoxal phosphate-dependent transferase, small domain / Pyridoxal phosphate-dependent transferase, major domain / Pyridoxal phosphate-dependent transferase / Alpha-Beta Complex / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
7-KETO-8-AMINOPELARGONIC ACID / PYRIDOXAL-5'-PHOSPHATE / Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Similarity search - Component
Biological speciesESCHERICHIA COLI BL21 (bacteria)
MethodX-RAY DIFFRACTION / OTHER / Resolution: 2.7 Å
AuthorsKaeck, H. / Sandmark, J. / Gibson, K.J. / Lindqvist, Y. / Schneider, G.
CitationJournal: J.Mol.Biol. / Year: 1999
Title: Crystal Structure of Diaminopelargonic Acid Synthase; Evolutionary Relationships between Pyridoxal-5'-Phosphate Dependent Enzymes
Authors: Kack, H. / Sandmark, J. / Gibson, K.J. / Schneider, G. / Lindqvist, Y.
History
DepositionJun 21, 1999Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 22, 2000Provider: repository / Type: Initial release
Revision 1.1May 8, 2011Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Version format compliance
Revision 1.3Jul 12, 2017Group: Data collection / Category: diffrn_source / Item: _diffrn_source.type
Revision 1.4Oct 24, 2018Group: Data collection / Source and taxonomy / Category: entity_src_gen
Item: _entity_src_gen.gene_src_strain / _entity_src_gen.pdbx_gene_src_ncbi_taxonomy_id / _entity_src_gen.pdbx_gene_src_scientific_name
Revision 1.5May 8, 2019Group: Data collection / Derived calculations / Experimental preparation
Category: exptl_crystal_grow / struct_conn
Item: _exptl_crystal_grow.temp / _struct_conn.pdbx_leaving_atom_flag

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: 7,8-DIAMINOPELARGONIC ACID SYNTHASE
B: 7,8-DIAMINOPELARGONIC ACID SYNTHASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5368
Polymers94,6212
Non-polymers9156
Water1,69394
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11060 Å2
ΔGint-99 kcal/mol
Surface area26810 Å2
MethodPISA
Unit cell
Length a, b, c (Å)57.970, 55.940, 120.840
Angle α, β, γ (deg.)90.00, 95.69, 90.00
Int Tables number4
Space group name H-MP1211
Noncrystallographic symmetry (NCS)NCS oper: (Code: given
Matrix: (-0.99995, 0.01019, 0.0007), (0.01019, 0.99051, 0.13706), (0.0007, 0.13706, -0.99056)
Vector: -48.6763, -11.998, 177.85899)

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Components

#1: Protein 7,8-DIAMINOPELARGONIC ACID SYNTHASE


Mass: 47310.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) ESCHERICHIA COLI BL21(DE3) (bacteria) / Cellular location: CYTOPLASM / Gene: BIOA / Plasmid: PET24 / Cellular location (production host): CYTOPLASM / Gene (production host): BIOA / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21(DE3)
References: UniProt: P12995, adenosylmethionine-8-amino-7-oxononanoate transaminase
#2: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Chemical ChemComp-KAP / 7-KETO-8-AMINOPELARGONIC ACID


Mass: 187.236 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C9H17NO3
#4: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 94 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsPYRIDOXAL-5'-PHOSPHATE IS BOUND TO LYS 274 IN BOTH CHAINS
Sequence detailsFROM THE ELECTRON DENSITY TRP14 IS REINTERPRETED AS LEUCINE

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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: 2.06 Å3/Da / Density % sol: 30 %
Crystal growTemperature: 293 K / pH: 7.5
Details: 25% PEG-4000, 20% MPD, 100MM HEPES PH7.5, 5MM KAPA (7-KETO-8-AMINOPELARGONIC ACID), 20 DEGREES C, MICROSEEDING., pH 7.50
Crystal grow
*PLUS
pH: 7.3 / Method: vapor diffusion
Details: drop consists of equal volume of protein and precipitant solutions
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDDetails
110 mg/mlprotein1drop
221 %PEG40001reservoirprecipitant
312 %2-propanol1reservoirprecipitant

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU FR-D / Wavelength: 1.5418
DetectorType: MARRESEARCH / Detector: IMAGE PLATE / Date: Oct 15, 1998
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.7→20 Å / Num. obs: 21479 / % possible obs: 99.9 % / Observed criterion σ(I): 2 / Redundancy: 5.8 % / Biso Wilson estimate: 42.6 Å2 / Rsym value: 0.104 / Net I/σ(I): 17.6
Reflection shellResolution: 2.7→2.82 Å / Mean I/σ(I) obs: 5.4 / Rsym value: 0.326 / % possible all: 99.7
Reflection
*PLUS
Num. measured all: 124908 / Rmerge(I) obs: 0.104
Reflection shell
*PLUS
% possible obs: 99.7 % / Rmerge(I) obs: 0.326

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Processing

Software
NameClassification
REFMACrefinement
DENZOdata reduction
SCALEPACKdata scaling
CCP4phasing
RefinementMethod to determine structure: OTHER / Resolution: 2.7→20 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: DUE TO DISORDERED MAINCHAIN THE FOLLOWING RESIDUES WERE REMOVED FROM THE MODEL OF CHAIN A: SER 160, MET 161, HIS 162, SER 163, LEU 164, TRP 165, LYS 166, GLY 167, TYR 168, ASP 183, GLY 300, ...Details: DUE TO DISORDERED MAINCHAIN THE FOLLOWING RESIDUES WERE REMOVED FROM THE MODEL OF CHAIN A: SER 160, MET 161, HIS 162, SER 163, LEU 164, TRP 165, LYS 166, GLY 167, TYR 168, ASP 183, GLY 300, ALA 301, GLN 429 DUE TO DISORDERED MAINCHAIN THE FOLLOWING RESIDUES WERE REMOVED FROM THE MODEL OF CHAIN B: SER 160, MET 161, HIS 162, SER 163, LEU 164, TRP 165, LYS 166, GLY 167, TYR 168, ASP 183, GLY 184, GLY 300, ALA 301, GLN 429
RfactorNum. reflection% reflectionSelection details
Rfree0.279 -5 %RANDOM
Rwork0.225 ---
obs-21479 99.9 %-
Displacement parametersBiso mean: 51.8 Å2
Refinement stepCycle: LAST / Resolution: 2.7→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6398 0 58 94 6550
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.0090.02
X-RAY DIFFRACTIONp_angle_d0.0330.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.030.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it1.9773
X-RAY DIFFRACTIONp_mcangle_it3.2545
X-RAY DIFFRACTIONp_scbond_it6.4066
X-RAY DIFFRACTIONp_scangle_it8.138
X-RAY DIFFRACTIONp_plane_restr0.0174
X-RAY DIFFRACTIONp_chiral_restr0.1130.15
X-RAY DIFFRACTIONp_singtor_nbd0.1880.3
X-RAY DIFFRACTIONp_multtor_nbd0.2620.3
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.180.3
X-RAY DIFFRACTIONp_planar_tor2.97
X-RAY DIFFRACTIONp_staggered_tor18.715
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor30.420
X-RAY DIFFRACTIONp_special_tor15

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