HEADER TRANSFERASE 02-DEC-99 1DJ9 TITLE CRYSTAL STRUCTURE OF 8-AMINO-7-OXONANOATE SYNTHASE (OR 7-KETO- TITLE 2 8AMINIPELARGONATE OR KAPA SYNTHASE) COMPLEXED WITH PLP AND THE TITLE 3 PRODUCT 8(S)-AMINO-7-OXONANONOATE (OR KAPA). THE ENZYME OF BIOTIN TITLE 4 BIOSYNTHETIC PATHWAY. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 8-AMINO-7-OXONONANOATE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: 7-KAP SYNTHETASE; COMPND 5 EC: 2.3.1.47 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562 KEYWDS 8-AMINO-7-OXONONANOATE SYNTHASE, BIOTIN, PYRIDOXAL-5'-PHOSPHATE, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR S.P.WEBSTER,D.ALEXEEV,D.J.CAMPOPIANO,R.M.WATT,M.ALEXEEVA,L.SAWYER, AUTHOR 2 R.L.BAXTER REVDAT 6 07-FEB-24 1DJ9 1 REMARK LINK REVDAT 5 04-OCT-17 1DJ9 1 REMARK REVDAT 4 13-JUL-11 1DJ9 1 VERSN REVDAT 3 24-FEB-09 1DJ9 1 VERSN REVDAT 2 01-APR-03 1DJ9 1 JRNL REVDAT 1 06-DEC-00 1DJ9 0 JRNL AUTH S.P.WEBSTER,D.ALEXEEV,D.J.CAMPOPIANO,R.M.WATT,M.ALEXEEVA, JRNL AUTH 2 L.SAWYER,R.L.BAXTER JRNL TITL MECHANISM OF 8-AMINO-7-OXONONANOATE SYNTHASE: SPECTROSCOPIC, JRNL TITL 2 KINETIC, AND CRYSTALLOGRAPHIC STUDIES. JRNL REF BIOCHEMISTRY V. 39 516 2000 JRNL REFN ISSN 0006-2960 JRNL PMID 10642176 JRNL DOI 10.1021/BI991620J REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH D.ALEXEEV,M.ALEXEEVA,R.L.BAXTER,S.P.WEBSTER,L.SAWYER REMARK 1 TITL THE CRYSTAL STRUCTURE OF 8-AMINO-7-OXONONANOATE SYNTHASE: A REMARK 1 TITL 2 BACTERIAL PLP- DEPENDENT, ACYL-COA-CONDENSING ENZYME REMARK 1 REF J.MOL.BIOL. V. 284 401 1998 REMARK 1 REFN ISSN 0022-2836 REMARK 1 DOI 10.1006/JMBI.1998.2086 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 10.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.212 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.212 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.278 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 820 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 27177 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.197 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 2284 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2912 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 337 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 3208.0 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 0.00 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : NULL REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 1320 REMARK 3 NUMBER OF RESTRAINTS : 1230 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.007 REMARK 3 ANGLE DISTANCES (A) : 0.020 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.025 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.030 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.030 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.000 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.000 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.100 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.000 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1DJ9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-DEC-99. REMARK 100 THE DEPOSITION ID IS D_1000010128. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 01-JAN-98 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX7.2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.488 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 27822 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 31.620 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.06500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.06 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.5 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.45200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: AB INITIO REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.39 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.00 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULPHATE, SODIUM CHLORIDE, REMARK 280 BIS-TRIS PROPANE BUFFER, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 289.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 1 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -Y,-X,-Z+2/3 REMARK 290 5555 -X+Y,Y,-Z+1/3 REMARK 290 6555 X,X-Y,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 67.25667 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 134.51333 REMARK 290 SMTRY1 4 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 134.51333 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 67.25667 REMARK 290 SMTRY1 6 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA,PQS REMARK 350 TOTAL BURIED SURFACE AREA: 11620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25520 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -141.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 67.25667 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A1190 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1292 LIES ON A SPECIAL POSITION. REMARK 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 MET A 1 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 CD2 LEU A 332 OE1 GLU A 336 1.22 REMARK 500 CD2 LEU A 332 CD GLU A 336 1.51 REMARK 500 CD1 LEU A 332 CB ALA A 335 1.60 REMARK 500 O ASN A 328 N ARG A 330 1.72 REMARK 500 ND2 ASN A 328 O LEU A 332 1.93 REMARK 500 ND2 ASN A 328 C LEU A 332 1.96 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 130 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 292 CD - NE - CZ ANGL. DEV. = -11.8 DEGREES REMARK 500 ARG A 292 NE - CZ - NH1 ANGL. DEV. = -5.0 DEGREES REMARK 500 ARG A 292 NE - CZ - NH2 ANGL. DEV. = 4.2 DEGREES REMARK 500 GLN A 333 C - N - CA ANGL. DEV. = 31.2 DEGREES REMARK 500 LEU A 334 C - N - CA ANGL. DEV. = 19.6 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ILE A 71 -83.85 -102.78 REMARK 500 VAL A 79 -113.24 -124.92 REMARK 500 LYS A 236 -111.11 -108.80 REMARK 500 VAL A 240 -111.82 -130.10 REMARK 500 LEU A 313 47.98 -87.27 REMARK 500 ALA A 314 81.16 -26.99 REMARK 500 ASP A 315 93.07 -37.89 REMARK 500 ASP A 327 130.80 89.64 REMARK 500 ASN A 328 116.10 164.21 REMARK 500 SER A 329 77.56 -50.89 REMARK 500 ARG A 330 98.22 -29.15 REMARK 500 ALA A 331 -56.40 169.19 REMARK 500 GLN A 333 147.45 101.11 REMARK 500 ALA A 355 -143.56 89.57 REMARK 500 ASN A 383 111.33 45.69 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLU A 336 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 500 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 179 OG REMARK 620 2 KAM A 400 N9C 142.1 REMARK 620 3 KAM A 400 O3 72.3 69.8 REMARK 620 4 KAM A 400 O7C 132.1 66.9 115.6 REMARK 620 5 HOH A1069 O 64.5 136.7 119.1 72.0 REMARK 620 6 HOH A1092 O 104.5 95.6 120.8 108.7 110.3 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE KAM A 400 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1BS0 RELATED DB: PDB REMARK 900 PLP-FREE APO-FORM OF THE ENZYME DBREF 1DJ9 A 1 384 UNP P12998 BIOF_ECOLI 1 384 SEQRES 1 A 384 MET SER TRP GLN GLU LYS ILE ASN ALA ALA LEU ASP ALA SEQRES 2 A 384 ARG GLY ALA ALA ASP ALA LEU ARG ARG ARG TYR PRO VAL SEQRES 3 A 384 ALA GLN GLY ALA GLY ARG TRP LEU VAL ALA ASP ASP ARG SEQRES 4 A 384 GLN TYR LEU ASN PHE SER SER ASN ASP TYR LEU GLY LEU SEQRES 5 A 384 SER HIS HIS PRO GLN ILE ILE ARG ALA TRP GLN GLN GLY SEQRES 6 A 384 ALA GLU GLN PHE GLY ILE GLY SER GLY GLY SER GLY HIS SEQRES 7 A 384 VAL SER GLY TYR SER VAL VAL HIS GLN ALA LEU GLU GLU SEQRES 8 A 384 GLU LEU ALA GLU TRP LEU GLY TYR SER ARG ALA LEU LEU SEQRES 9 A 384 PHE ILE SER GLY PHE ALA ALA ASN GLN ALA VAL ILE ALA SEQRES 10 A 384 ALA MET MET ALA LYS GLU ASP ARG ILE ALA ALA ASP ARG SEQRES 11 A 384 LEU SER HIS ALA SER LEU LEU GLU ALA ALA SER LEU SER SEQRES 12 A 384 PRO SER GLN LEU ARG ARG PHE ALA HIS ASN ASP VAL THR SEQRES 13 A 384 HIS LEU ALA ARG LEU LEU ALA SER PRO CYS PRO GLY GLN SEQRES 14 A 384 GLN MET VAL VAL THR GLU GLY VAL PHE SER MET ASP GLY SEQRES 15 A 384 ASP SER ALA PRO LEU ALA GLU ILE GLN GLN VAL THR GLN SEQRES 16 A 384 GLN HIS ASN GLY TRP LEU MET VAL ASP ASP ALA HIS GLY SEQRES 17 A 384 THR GLY VAL ILE GLY GLU GLN GLY ARG GLY SER CYS TRP SEQRES 18 A 384 LEU GLN LYS VAL LYS PRO GLU LEU LEU VAL VAL THR PHE SEQRES 19 A 384 GLY LYS GLY PHE GLY VAL SER GLY ALA ALA VAL LEU CYS SEQRES 20 A 384 SER SER THR VAL ALA ASP TYR LEU LEU GLN PHE ALA ARG SEQRES 21 A 384 HIS LEU ILE TYR SER THR SER MET PRO PRO ALA GLN ALA SEQRES 22 A 384 GLN ALA LEU ARG ALA SER LEU ALA VAL ILE ARG SER ASP SEQRES 23 A 384 GLU GLY ASP ALA ARG ARG GLU LYS LEU ALA ALA LEU ILE SEQRES 24 A 384 THR ARG PHE ARG ALA GLY VAL GLN ASP LEU PRO PHE THR SEQRES 25 A 384 LEU ALA ASP SER CYS SER ALA ILE GLN PRO LEU ILE VAL SEQRES 26 A 384 GLY ASP ASN SER ARG ALA LEU GLN LEU ALA GLU LYS LEU SEQRES 27 A 384 ARG GLN GLN GLY CYS TRP VAL THR GLY ILE ARG PRO PRO SEQRES 28 A 384 THR VAL PRO ALA GLY ILE ALA ARG LEU ARG LEU THR LEU SEQRES 29 A 384 THR ALA ALA HIS GLU MET GLN ASP ILE ASP ARG LEU LEU SEQRES 30 A 384 GLU VAL LEU HIS GLY ASN GLY HET SO4 A 401 5 HET SO4 A 402 5 HET MG A 500 1 HET KAM A 400 28 HETNAM SO4 SULFATE ION HETNAM MG MAGNESIUM ION HETNAM KAM N-[7-KETO-8-AMINOPELARGONIC ACID]-[3-HYDROXY-2-METHYL- HETNAM 2 KAM 5-PHOSPHONOOXYMETHYL-PYRIDIN-4-YL-METHANE] HETSYN KAM N-PYRIDOXYL-7-KETO-8-AMINOPELARGONIC ACID-5'- HETSYN 2 KAM MONOPHOSPHATE FORMUL 2 SO4 2(O4 S 2-) FORMUL 4 MG MG 2+ FORMUL 5 KAM C17 H27 N2 O8 P FORMUL 6 HOH *337(H2 O) HELIX 1 1 SER A 2 ALA A 17 1 16 HELIX 2 2 GLY A 51 HIS A 54 5 4 HELIX 3 3 HIS A 55 GLY A 70 1 16 HELIX 4 4 SER A 83 GLY A 98 1 16 HELIX 5 5 SER A 107 MET A 120 1 14 HELIX 6 6 HIS A 133 SER A 143 1 11 HELIX 7 7 ASP A 154 SER A 164 1 11 HELIX 8 8 PRO A 186 HIS A 197 1 12 HELIX 9 9 GLY A 213 ARG A 217 5 5 HELIX 10 10 GLY A 218 LYS A 224 1 7 HELIX 11 11 SER A 248 ALA A 259 1 12 HELIX 12 12 ALA A 259 TYR A 264 1 6 HELIX 13 13 PRO A 269 SER A 285 1 17 HELIX 14 14 SER A 285 VAL A 306 1 22 HELIX 15 15 GLN A 307 LEU A 309 5 3 HELIX 16 16 ILE A 324 ASN A 328 5 5 HELIX 17 17 LEU A 332 GLN A 341 1 10 HELIX 18 18 GLU A 369 GLY A 382 1 14 SHEET 1 A 3 TRP A 33 ALA A 36 0 SHEET 2 A 3 ARG A 39 ASN A 43 -1 N ARG A 39 O ALA A 36 SHEET 3 A 3 CYS A 343 TRP A 344 1 N TRP A 344 O LEU A 42 SHEET 1 B 7 ARG A 101 PHE A 105 0 SHEET 2 B 7 ALA A 243 CYS A 247 -1 O ALA A 243 N PHE A 105 SHEET 3 B 7 LEU A 229 THR A 233 -1 O LEU A 230 N LEU A 246 SHEET 4 B 7 TRP A 200 ASP A 204 1 O LEU A 201 N LEU A 229 SHEET 5 B 7 GLN A 170 GLU A 175 1 O GLN A 170 N TRP A 200 SHEET 6 B 7 ARG A 125 ASP A 129 1 O ARG A 125 N MET A 171 SHEET 7 B 7 GLN A 146 PHE A 150 1 O GLN A 146 N ILE A 126 SHEET 1 C 2 ILE A 320 GLN A 321 0 SHEET 2 C 2 LEU A 362 THR A 363 -1 O LEU A 362 N GLN A 321 LINK OG SER A 179 MG MG A 500 1555 1555 2.61 LINK N9C KAM A 400 MG MG A 500 1555 1555 2.08 LINK O3 KAM A 400 MG MG A 500 1555 1555 2.09 LINK O7C KAM A 400 MG MG A 500 1555 1555 2.70 LINK MG MG A 500 O HOH A1069 1555 1555 2.65 LINK MG MG A 500 O HOH A1092 1555 1555 2.18 CISPEP 1 GLN A 333 LEU A 334 0 1.92 CISPEP 2 PRO A 350 PRO A 351 0 6.07 SITE 1 AC1 5 LEU A 147 ARG A 148 ARG A 149 HOH A1203 SITE 2 AC1 5 HOH A1245 SITE 1 AC2 5 ARG A 22 ARG A 23 ARG A 101 LEU A 256 SITE 2 AC2 5 HOH A1238 SITE 1 AC3 4 SER A 179 KAM A 400 HOH A1069 HOH A1092 SITE 1 AC4 25 ARG A 21 SER A 76 SER A 107 GLY A 108 SITE 2 AC4 25 PHE A 109 HIS A 133 GLU A 175 SER A 179 SITE 3 AC4 25 ASP A 204 ALA A 206 HIS A 207 THR A 233 SITE 4 AC4 25 LYS A 236 ILE A 263 TYR A 264 SER A 265 SITE 5 AC4 25 THR A 266 ILE A 348 THR A 352 MG A 500 SITE 6 AC4 25 HOH A1004 HOH A1013 HOH A1092 HOH A1161 SITE 7 AC4 25 HOH A1237 CRYST1 58.890 58.890 201.770 90.00 90.00 120.00 P 31 1 2 6 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016981 0.009804 0.000000 0.00000 SCALE2 0.000000 0.019608 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004956 0.00000