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- PDB-1b9h: CRYSTAL STRUCTURE OF 3-AMINO-5-HYDROXYBENZOIC ACID (AHBA) SYNTHASE -

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Basic information

Entry
Database: PDB / ID: 1b9h
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 / polysaccharide biosynthetic process / transaminase activity / antibiotic biosynthetic process / pyridoxal phosphate binding / 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
PYRIDOXAL-5'-PHOSPHATE / 3-amino-5-hydroxybenzoate synthase
Similarity search - Component
Biological speciesAmycolatopsis mediterranei (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MIR / 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 1.3Dec 27, 2023Group: Data collection / Database references / Derived calculations
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / struct_conn / 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_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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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)42,5102
Polymers42,2631
Non-polymers2471
Water3,891216
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)85,0204
Polymers84,5252
Non-polymers4942
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area6860 Å2
ΔGint-22 kcal/mol
Surface area25800 Å2
MethodPISA, PQS
Unit cell
Length a, b, c (Å)89.700, 89.700, 127.700
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

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


Mass: 42262.625 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-PLP / PYRIDOXAL-5'-PHOSPHATE / VITAMIN B6 Phosphate


Mass: 247.142 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H10NO6P
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 216 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 3.51 Å3/Da / Density % sol: 60 %
Description: MAD DATA USED AS MIR EXPERIMENT, STATISTICS LISTED ARE FOR BEST MAD DATASET (IE NOT NATIVE)
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: ESRF / Beamline: BM14 / Wavelength: 1.5418,1.008,0.832
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
11.54181
21.0081
30.8321
ReflectionResolution: 1.7→99 Å / Num. obs: 65659 / % possible obs: 99.6 % / Redundancy: 1.9 % / Rsym value: 3.8 / Net I/σ(I): 18.6
Reflection shellResolution: 1.7→1.76 Å / Rsym value: 16.6 / % possible all: 100
Reflection
*PLUS
Rmerge(I) obs: 0.037
Reflection shell
*PLUS
% possible obs: 100 % / Rmerge(I) obs: 0.203 / Mean I/σ(I) obs: 2.6

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Processing

Software
NameClassification
SHARPphasing
REFMACrefinement
RefinementMethod to determine structure: MIR / Resolution: 2→10 Å / Cross valid method: THROUGHOUT / σ(F): 0
Details: XPLOR USED IN EARLIER STAGES OF REFINEMENT. RESIDUE 1 (MET) IS NOT PRESENT IN THE PROTEIN. RESIDUES 2-4 ARE NOT MODELED IN THE STRUCTURE (POOR ELECTRON DENSITY)
RfactorNum. reflection% reflectionSelection details
Rfree0.252 1994 5 %RANDOM
Rwork0.215 ---
obs0.218 39738 98.8 %-
Refinement stepCycle: LAST / Resolution: 2→10 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2940 0 15 216 3171
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONp_bond_d0.015
X-RAY DIFFRACTIONp_angle_d0.039
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_restr0.024
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
Software
*PLUS
Name: REFMAC / Classification: refinement
Refinement
*PLUS
Highest resolution: 2 Å / σ(F): 0 / % reflection Rfree: 5 %
Solvent computation
*PLUS
Displacement parameters
*PLUS

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