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- PDB-5uc7: Crystal structure of BioA / 7,8-diaminopelargonic acid aminotrans... -

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Basic information

Entry
Database: PDB / ID: 5uc7
TitleCrystal structure of BioA / 7,8-diaminopelargonic acid aminotransferase / DAPA synthase from Citrobacter rodentium, PLP complex
ComponentsAdenosylmethionine-8-amino-7-oxononanoate aminotransferase
KeywordsTRANSFERASE / AMINOTRANSFERASE / PYRIDOXAL-5'-PHOSPHATE / PLP-DEPENDENT FOLD TYPE I SUB CLASS II AMINOTRANSFERASE / BIOTIN BIOSYNTHESIS / 7 / 8-diaminopelargonic acid / DAPA / STRUCTURAL GENOMICS / CSGID / CENTER FOR STRUCTURAL GENOMICS OF INFECTIOUS DISEASES / NIAID / NATIONAL INSTITUTE OF ALLERGY AND INFECTIOUS DISEASES
Function / homology
Function and homology information


adenosylmethionine-8-amino-7-oxononanoate transaminase / adenosylmethionine-8-amino-7-oxononanoate transaminase activity / biotin biosynthetic process / pyridoxal phosphate binding / 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
D(-)-TARTARIC ACID / Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Similarity search - Component
Biological speciesCitrobacter rodentium (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.835 Å
AuthorsStogios, P.J. / Evdokimova, E. / Di Leo, R. / Savchenko, A. / Anderson, W.F. / Center for Structural Genomics of Infectious Diseases (CSGID)
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)HHSN272201200026C United States
CitationJournal: To Be Published
Title: Crystal structure of BioA / 7,8-diaminopelargonic acid aminotransferase / DAPA synthase from Citrobacter rodentium, PLP complex
Authors: Stogios, P.J.
History
DepositionDec 21, 2016Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 25, 2017Provider: repository / Type: Initial release
Revision 1.1Sep 27, 2017Group: Author supporting evidence / Category: pdbx_audit_support
Item: _pdbx_audit_support.country / _pdbx_audit_support.funding_organization
Revision 1.2Dec 11, 2019Group: Author supporting evidence / Category: pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Oct 4, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.4Nov 15, 2023Group: Data collection / Category: chem_comp_atom / chem_comp_bond / Item: _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_2

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,0143
Polymers47,7141
Non-polymers3002
Water8,107450
1
A: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
hetero molecules

A: Adenosylmethionine-8-amino-7-oxononanoate aminotransferase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)96,0286
Polymers95,4272
Non-polymers6004
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_665-x+1,-y+1,z1
Buried area11740 Å2
ΔGint-82 kcal/mol
Surface area27650 Å2
MethodPISA
Unit cell
Length a, b, c (Å)75.369, 88.306, 63.274
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number18
Space group name H-MP21212
Components on special symmetry positions
IDModelComponents
11A-651-

HOH

21A-684-

HOH

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Components

#1: Protein Adenosylmethionine-8-amino-7-oxononanoate aminotransferase / 7 / 8-diamino-pelargonic acid aminotransferase / 8-diaminononanoate synthase / Diaminopelargonic acid synthase


Mass: 47713.625 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Citrobacter rodentium (bacteria) / Strain: ICC168 / Gene: bioA, ROD_07751 / Plasmid: pMCSG53 / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)Gold
References: UniProt: D2TPI3, adenosylmethionine-8-amino-7-oxononanoate transaminase
#2: Chemical ChemComp-TAR / D(-)-TARTARIC ACID


Mass: 150.087 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C4H6O6
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 450 / 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: 2.23 Å3/Da / Density % sol: 44.78 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.2 M ammonium tartrate pH 7, 20% (w/v) PEG3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 21-ID-G / Wavelength: 0.97856 Å
DetectorType: MARMOSAIC 300 mm CCD / Detector: CCD / Date: Oct 14, 2016
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97856 Å / Relative weight: 1
ReflectionResolution: 1.835→51.43 Å / Num. obs: 36804 / % possible obs: 97.8 % / Redundancy: 5.4 % / CC1/2: 0.998 / Rmerge(I) obs: 0.104 / Rsym value: 0.104 / Net I/σ(I): 12.5
Reflection shellResolution: 1.835→1.841 Å / Redundancy: 4.8 % / Rmerge(I) obs: 0.778 / Mean I/σ(I) obs: 2.1 / Num. measured obs: 1718 / CC1/2: 0.661 / % possible all: 90.6

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Processing

Software
NameVersionClassification
PHENIXdev_2481refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
PHENIXmodel building
Cootmodel building
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1QJ5

1qj5


Resolution: 1.835→44.153 Å / SU ML: 0.19 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 19
RfactorNum. reflection% reflectionSelection details
Rfree0.1984 1999 5.44 %RANDOM
Rwork0.1517 ---
obs0.1542 36737 97.62 %-
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Refinement stepCycle: LAST / Resolution: 1.835→44.153 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3342 0 20 450 3812
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0183504
X-RAY DIFFRACTIONf_angle_d1.414770
X-RAY DIFFRACTIONf_dihedral_angle_d19.2761296
X-RAY DIFFRACTIONf_chiral_restr0.109521
X-RAY DIFFRACTIONf_plane_restr0.01625
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.8353-1.88120.3171340.24692320X-RAY DIFFRACTION93
1.8812-1.93210.28411110.23451943X-RAY DIFFRACTION78
1.9321-1.98890.28151420.21442463X-RAY DIFFRACTION100
1.9889-2.05310.22821460.18282524X-RAY DIFFRACTION100
2.0531-2.12650.23341440.16452505X-RAY DIFFRACTION100
2.1265-2.21160.21681440.15032513X-RAY DIFFRACTION100
2.2116-2.31230.17211440.15242494X-RAY DIFFRACTION100
2.3123-2.43420.21451460.14932542X-RAY DIFFRACTION100
2.4342-2.58670.21041460.15492533X-RAY DIFFRACTION100
2.5867-2.78640.21931450.14562525X-RAY DIFFRACTION100
2.7864-3.06670.18841480.14682548X-RAY DIFFRACTION100
3.0667-3.51030.17181470.13792570X-RAY DIFFRACTION100
3.5103-4.4220.15791480.11842581X-RAY DIFFRACTION100
4.422-44.16580.17951540.1472677X-RAY DIFFRACTION98
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)
11.5556-0.4447-0.04271.0520.13590.3241-0.0045-0.0763-0.12210.05930.0081-0.04950.03880.0186-0.00210.0764-0.0036-0.00030.0970.01840.095138.453136.34774.4929
23.0791.708-2.2073.95451.36684.2093-0.1026-0.7379-0.55791.0988-0.0479-0.66440.43240.59420.14330.49830.0656-0.0580.44710.07140.286731.256638.2530.0618
31.459-0.1604-0.10580.61590.29932.62630.0292-0.5424-0.43770.5972-0.00990.22470.4554-0.1529-0.0190.4232-0.04550.10370.34770.08480.277720.568329.847625.4943
41.9323-0.2012-0.12741.286-0.77040.68660.0171-0.28240.17630.26970.0340.1635-0.1694-0.0346-0.00620.11460.00740.03760.1482-0.01540.129124.517343.070410.9545
52.6559-1.03110.19092.3849-0.48842.2294-0.0239-0.3134-0.35920.40720.0211-0.31430.25890.1162-0.00540.2176-0.008-0.05970.13610.04460.283237.42113.799211.1938
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid -1:109)
2X-RAY DIFFRACTION2(chain A and resid 110:179)
3X-RAY DIFFRACTION3(chain A and resid 180:276)
4X-RAY DIFFRACTION4(chain A and resid 277:338)
5X-RAY DIFFRACTION5(chain A and resid 339:429)

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