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- PDB-1b9i: CRYSTAL STRUCTURE OF 3-AMINO-5-HYDROXYBENZOIC ACID (AHBA) SYNTHASE -

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Basic information

Entry
Database: PDB / ID: 1b9i
TitleCRYSTAL STRUCTURE OF 3-AMINO-5-HYDROXYBENZOIC ACID (AHBA) SYNTHASE
ComponentsPROTEIN (3-AMINO-5-HYDROXYBENZOIC ACID SYNTHASE)
KeywordsRIFAMYCIN BIOSYNTHESIS (RIFD GENE)
Function / homology
Function and homology information


3-amino-5-hydroxybenzoate synthase / Transferases; Transferring nitrogenous groups; Transaminases / antibiotic biosynthetic process / transferase activity / lyase activity
Similarity search - Function
DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / 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 ...DegT/DnrJ/EryC1/StrS aminotransferase / DegT/DnrJ/EryC1/StrS aminotransferase family / 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
3-[O-PHOSPHONOPYRIDOXYL]--AMINO-BENZOIC ACID / 3-amino-5-hydroxybenzoate synthase
Similarity search - Component
Biological speciesAmycolatopsis mediterranei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsEads, J.C. / Beeby, M. / Scapin, G. / Yu, T.-W. / Floss, H.G.
CitationJournal: Biochemistry / Year: 1999
Title: Crystal structure of 3-amino-5-hydroxybenzoic acid (AHBA) synthase.
Authors: Eads, J.C. / Beeby, M. / Scapin, G. / Yu, T.W. / Floss, H.G.
History
DepositionFeb 11, 1999Deposition site: PDBE / Processing site: RCSB
Revision 1.0Aug 13, 1999Provider: repository / Type: Initial release
Revision 1.1Apr 26, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Derived calculations / Version format compliance
Revision 1.3Jun 13, 2018Group: Data collection / Category: diffrn_radiation / diffrn_source
Item: _diffrn_radiation.pdbx_diffrn_protocol / _diffrn_source.pdbx_wavelength_list
Revision 1.4Dec 21, 2022Group: Data collection / Database references / Derived calculations
Category: database_2 / diffrn_radiation_wavelength ...database_2 / diffrn_radiation_wavelength / 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 / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.5May 22, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: PROTEIN (3-AMINO-5-HYDROXYBENZOIC ACID SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)42,6172
Polymers42,2491
Non-polymers3681
Water3,387188
1
A: PROTEIN (3-AMINO-5-HYDROXYBENZOIC ACID SYNTHASE)
hetero molecules

A: PROTEIN (3-AMINO-5-HYDROXYBENZOIC ACID SYNTHASE)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)85,2344
Polymers84,4972
Non-polymers7372
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area7580 Å2
ΔGint-18 kcal/mol
Surface area24920 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)89.630, 89.630, 126.570
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-406-

HOH

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Components

#1: Protein PROTEIN (3-AMINO-5-HYDROXYBENZOIC ACID SYNTHASE) / AHBA SYNTHASE


Mass: 42248.598 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Amycolatopsis mediterranei (bacteria) / Plasmid: PRSETB(EAHBA6) / Production host: Escherichia coli (E. coli) / References: UniProt: O52552
#2: Chemical ChemComp-PXG / 3-[O-PHOSPHONOPYRIDOXYL]--AMINO-BENZOIC ACID


Mass: 368.278 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C15H17N2O7P
#3: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2

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Sample preparation

CrystalDensity Matthews: 3.47 Å3/Da / Density % sol: 60 % / Description: IN-HOUSE (CUKA) DATA MERGED WITH SRS DATA
Crystal growpH: 7.5 / Details: pH 7.5
Crystal
*PLUS
Crystal grow
*PLUS
Temperature: 18 ℃ / Method: vapor diffusion, hanging drop
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
111 mg/mlprotein1drop
250 mMHEPES1drop
30.05 %1dropNaN3
40.5 mMPLP1drop
5100 mMHEPES1reservoir
61.7 Mammonium sulfate1reservoir
73-8 %PEG4001reservoir

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Data collection

DiffractionMean temperature: 133 K
Diffraction sourceSource: SYNCHROTRON / Site: SRS / Beamline: PX7.2 / Wavelength: 1.488 / Wavelength: 1.4888 Å
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.4881
21.48881
ReflectionResolution: 2→42.3 Å / Num. obs: 38950 / % possible obs: 96.3 % / Redundancy: 6.6 % / Rmerge(I) obs: 0.089 / Net I/σ(I): 5.1
Reflection shellResolution: 2→2.11 Å / Redundancy: 3.8 % / Rmerge(I) obs: 0.177 / Mean I/σ(I) obs: 4 / % possible all: 89
Reflection shell
*PLUS
% possible obs: 89 %

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Processing

SoftwareName: REFMAC / Classification: refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→20 Å / Cross valid method: THROUGHOUT / σ(F): 0 / Details: XPLOR USED IN EARLIER STAGES OF REFINEMENT
RfactorNum. reflection% reflectionSelection details
Rfree0.272 1936 5 %RANDOM
Rwork0.222 ---
obs0.225 38865 96 %-
Refinement stepCycle: LAST / Resolution: 2→20 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2935 0 25 188 3148
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.016
X-RAY DIFFRACTIONp_angle_d0.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it
X-RAY DIFFRACTIONp_mcangle_it
X-RAY DIFFRACTIONp_scbond_it
X-RAY DIFFRACTIONp_scangle_it
X-RAY DIFFRACTIONp_plane_restr
X-RAY DIFFRACTIONp_chiral_restr
X-RAY DIFFRACTIONp_singtor_nbd
X-RAY DIFFRACTIONp_multtor_nbd
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd
X-RAY DIFFRACTIONp_planar_tor
X-RAY DIFFRACTIONp_staggered_tor
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor
X-RAY DIFFRACTIONp_special_tor
Refinement
*PLUS
Highest resolution: 2 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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