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- PDB-1mlz: Crystal Structure of 7,8-Diaminopelargonic Acid Synthase in compl... -

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Basic information

Entry
Database: PDB / ID: 1mlz
TitleCrystal Structure of 7,8-Diaminopelargonic Acid Synthase in complex with the trans-isomer of amiclenomycin.
Components7,8-diamino-pelargonic acid aminotransferase
KeywordsTRANSFERASE / Aminotransferase / Fold type I / subclass II / amiclenomycin
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
PYRIDOXAL-5'-PHOSPHATE / TRANS-AMICLENOMYCIN / Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Similarity search - Component
Biological speciesEscherichia coli (E. coli)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.15 Å
AuthorsSandmark, J. / Mann, S. / Marquet, A. / Schneider, G.
CitationJournal: J.Biol.Chem. / Year: 2002
Title: Structural basis for the inhibition of the biosynthesis of biotin by the antibiotic amiclenomycin
Authors: Sandmark, J. / Mann, S. / Marquet, A. / Schneider, G.
History
DepositionSep 2, 2002Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 4, 2002Provider: repository / Type: Initial release
Revision 1.1Apr 28, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Mar 7, 2018Group: Advisory / Data collection
Category: diffrn_source / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues
Item: _diffrn_source.pdbx_synchrotron_site
Revision 1.4Feb 14, 2024Group: Advisory / Data collection ...Advisory / 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 / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / 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.pdbx_leaving_atom_flag / _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_conn.ptnr2_label_seq_id / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Remark 999sequence The crystallized protein differs from the Swissprot sequence at residue 14. Number 14 is a ...sequence The crystallized protein differs from the Swissprot sequence at residue 14. Number 14 is a leucin, while in the Swissprot sequence number 14 is a tryptophan. This is confirmed by DNA sequencing and was also reported for the original WT structure (1qj5).

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: 7,8-diamino-pelargonic acid aminotransferase
B: 7,8-diamino-pelargonic acid aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)95,5548
Polymers94,6212
Non-polymers9336
Water5,837324
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12760 Å2
ΔGint-110 kcal/mol
Surface area26730 Å2
MethodPISA
Unit cell
Length a, b, c (Å)128.034, 55.960, 116.001
Angle α, β, γ (deg.)90.00, 109.65, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein 7,8-diamino-pelargonic acid aminotransferase / Adenosylmethionine-8-amino-7-oxononanoate aminotransferase / DAPA aminotransferase


Mass: 47310.391 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli (E. coli) / Gene: bioA / Species (production host): Escherichia coli / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3)
References: UniProt: P12995, adenosylmethionine-8-amino-7-oxononanoate transaminase
#2: Chemical ChemComp-TZA / TRANS-AMICLENOMYCIN / 2-AMINO-4-(4-AMINO-CYCLOHEXA-2,5-DIENYL)-BUTYRIC ACID


Mass: 196.246 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H16N2O2
#3: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#4: Chemical ChemComp-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C8H10NO6P
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 324 / Source method: isolated from a natural source / Formula: H2O
Nonpolymer detailsA covalent adduct is formed between pyridoxal-5'-phosphate and the amiclenomycin in the A subunit. ...A covalent adduct is formed between pyridoxal-5'-phosphate and the amiclenomycin in the A subunit. In the B subunit the density for amiclenomycin is significantly weaker. The amiclenomycin molecule is modeled as non-covalently bound in the B subunit, but the model has high B factors and is not well supported by structural data. For a better view of the pyridoxal-5'-phosphate-amiclenomycin adduct see the A subunit in the structure of the enzyme in complex with the cis-isomer (PDB ID 1mly). For details see the primary citation.

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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: 2.07 Å3/Da / Density % sol: 40.49 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 7.5
Details: PEG4000, MPD, HEPES, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 294K
Crystal grow
*PLUS
Method: vapor diffusion / Details: Kack, H., (1998) Acta Crystallogr., D54, 1397.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
221 %PEG40001reservoir
312 %2-propanol1reservoir

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: MAX II / Beamline: I711 / Wavelength: 0.991 Å
DetectorType: MARRESEARCH / Detector: CCD / Date: May 10, 2001
RadiationMonochromator: Si(111) monochromator crystal / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.991 Å / Relative weight: 1
ReflectionResolution: 2.15→22.36 Å / Num. all: 41748 / Num. obs: 41748 / % possible obs: 98.6 % / Observed criterion σ(F): 0 / Observed criterion σ(I): 0 / Biso Wilson estimate: 31.2 Å2 / Rsym value: 0.066 / Net I/σ(I): 13.9
Reflection shellResolution: 2.15→2.27 Å / Mean I/σ(I) obs: 2.9 / Rsym value: 0.291 / % possible all: 96
Reflection
*PLUS
Lowest resolution: 20 Å / Num. obs: 38070 / Num. measured all: 112317 / Rmerge(I) obs: 0.066
Reflection shell
*PLUS
% possible obs: 96 % / Rmerge(I) obs: 0.291

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Processing

Software
NameVersionClassification
MOSFLMdata reduction
SCALAdata scaling
AMoREphasing
REFMAC5refinement
CCP4(SCALA)data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.15→22.36 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.923 / SU B: 9.138 / SU ML: 0.237 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.334 / ESU R Free: 0.219 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: In monomer A two stretches of residues are disordered, 159-169 and 186-192 resp. In monomer B three stretches of residues are disordered, 158-168, 189-194 and 296-301 resp. Residue 429 was ...Details: In monomer A two stretches of residues are disordered, 159-169 and 186-192 resp. In monomer B three stretches of residues are disordered, 158-168, 189-194 and 296-301 resp. Residue 429 was excluded from both monomers. A number of sidechains on the surface of the protein are disordered. The occupancy for these is estimated to 0 in most cases.
RfactorNum. reflection% reflectionSelection details
Rfree0.24028 2108 5 %RANDOM
Rwork0.20465 ---
all0.207 39635 --
obs0.207 39635 98.5 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.4 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.347 Å2
Baniso -1Baniso -2Baniso -3
1--2.28 Å20 Å2-2.69 Å2
2--2.67 Å20 Å2
3----2.19 Å2
Refinement stepCycle: LAST / Resolution: 2.15→22.36 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6587 0 60 324 6971
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0160.0216638
X-RAY DIFFRACTIONr_bond_other_d0.0040.026097
X-RAY DIFFRACTIONr_angle_refined_deg1.5831.9499002
X-RAY DIFFRACTIONr_angle_other_deg1.898314057
X-RAY DIFFRACTIONr_dihedral_angle_1_deg3.9373836
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.55151132
X-RAY DIFFRACTIONr_chiral_restr0.0920.2999
X-RAY DIFFRACTIONr_gen_planes_refined0.0120.027386
X-RAY DIFFRACTIONr_gen_planes_other0.0260.021364
X-RAY DIFFRACTIONr_nbd_refined0.2730.31581
X-RAY DIFFRACTIONr_nbd_other0.2210.35924
X-RAY DIFFRACTIONr_nbtor_other0.2890.513
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1740.5423
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.1780.57
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.250.313
X-RAY DIFFRACTIONr_symmetry_vdw_other0.2450.343
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.4010.56
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_mcbond_it0.6771.54209
X-RAY DIFFRACTIONr_mcangle_it1.2626714
X-RAY DIFFRACTIONr_scbond_it1.79532429
X-RAY DIFFRACTIONr_scangle_it2.9174.52288
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.205 Å / Total num. of bins used: 20 /
RfactorNum. reflection
Rfree0.379 158
Rwork0.292 2696
Refinement
*PLUS
Lowest resolution: 20 Å / Rfactor Rfree: 0.24 / Rfactor Rwork: 0.205
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONr_bond_d0.016
X-RAY DIFFRACTIONr_angle_d
X-RAY DIFFRACTIONr_angle_deg1.583

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