HEADER TRANSFERASE 30-MAY-19 6RV1 TITLE HUMAN ALANINE:GLYOXYLATE AMINOTRANSFERASE MAJOR ALLELE (AGT-MA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE--PYRUVATE AMINOTRANSFERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SPT,ALANINE--GLYOXYLATE AMINOTRANSFERASE,AGT; COMPND 5 EC: 2.6.1.51,2.6.1.44; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: AGXT, AGT1, SPAT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS AMINOTRANSFERASE, DETOXIFICATION, LIVER, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.GIARDINA,F.CUTRUZZOLA,B.CELLINI,D.MIRCO REVDAT 1 08-APR-20 6RV1 0 JRNL AUTH M.DINDO,S.GROTTELLI,G.ANNUNZIATO,G.GIARDINA,M.PIERONI, JRNL AUTH 2 G.PAMPALONE,A.FACCINI,F.CUTRUZZOLA,P.LAURINO,G.COSTANTINO, JRNL AUTH 3 B.CELLINI JRNL TITL CYCLOSERINE ENANTIOMERS ARE REVERSIBLE INHIBITORS OF HUMAN JRNL TITL 2 ALANINE:GLYOXYLATE AMINOTRANSFERASE: IMPLICATIONS FOR JRNL TITL 3 PRIMARY HYPEROXALURIA TYPE 1. JRNL REF BIOCHEM.J. V. 476 3751 2019 JRNL REFN ESSN 1470-8728 JRNL PMID 31794008 JRNL DOI 10.1042/BCJ20190507 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 11360 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.275 REMARK 3 R VALUE (WORKING SET) : 0.273 REMARK 3 FREE R VALUE : 0.316 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 608 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 822 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.4370 REMARK 3 BIN FREE R VALUE SET COUNT : 45 REMARK 3 BIN FREE R VALUE : 0.5080 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2611 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 2 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 110.3 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 6.91000 REMARK 3 B22 (A**2) : 6.91000 REMARK 3 B33 (A**2) : -13.83000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 1.476 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.465 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.660 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 41.397 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.931 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.915 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2692 ; 0.007 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2263 ; 0.003 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3697 ; 1.481 ; 1.630 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5197 ; 1.312 ; 1.565 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 378 ; 6.537 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 94 ;37.115 ;22.872 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 316 ;16.429 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 8 ; 9.534 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 380 ; 0.059 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3161 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 530 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6RV1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 31-MAY-19. REMARK 100 THE DEPOSITION ID IS D_1292102665. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-JUL-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 REMARK 200 MONOCHROMATOR : SI (111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.7.4 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12014 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 REMARK 200 RESOLUTION RANGE LOW (A) : 47.020 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 12.50 REMARK 200 R MERGE (I) : 0.09800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.18 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 13.40 REMARK 200 R MERGE FOR SHELL (I) : 2.39100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10-12% PEG 6K; 5% 2-METHYL-2,4 REMARK 280 -PENTANEDIOL (MPD); 0.1M MES PH 6.5, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 70.39850 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 44.66650 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 44.66650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 35.19925 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 44.66650 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 44.66650 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 105.59775 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 44.66650 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.66650 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.19925 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 44.66650 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.66650 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 105.59775 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 70.39850 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 7580 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -53.0 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 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -70.39850 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 465 ALA A 2 REMARK 465 SER A 3 REMARK 465 HIS A 4 REMARK 465 LYS A 5 REMARK 465 PRO A 353 REMARK 465 SER A 354 REMARK 465 THR A 355 REMARK 465 GLY A 356 REMARK 465 LYS A 390 REMARK 465 LYS A 391 REMARK 465 LEU A 392 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 6 CG CD1 CD2 REMARK 470 LEU A 7 CG CD1 CD2 REMARK 470 LYS A 12 CG CD CE NZ REMARK 470 LEU A 14 CG CD1 CD2 REMARK 470 LYS A 16 CG CD CE NZ REMARK 470 ASN A 22 CG OD1 ND2 REMARK 470 GLN A 23 CD OE1 NE2 REMARK 470 LEU A 24 CD1 CD2 REMARK 470 ILE A 37 CD1 REMARK 470 LYS A 51 CG CD CE NZ REMARK 470 ASP A 52 CG OD1 OD2 REMARK 470 GLN A 55 CG CD OE1 NE2 REMARK 470 GLU A 59 CD OE1 OE2 REMARK 470 LYS A 61 CG CD CE NZ REMARK 470 GLU A 62 CD OE1 OE2 REMARK 470 ILE A 64 CG1 CG2 CD1 REMARK 470 ARG A 71 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 78 CD1 REMARK 470 PHE A 100 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LEU A 101 CG CD1 CD2 REMARK 470 ILE A 107 N REMARK 470 GLN A 110 CG CD OE1 NE2 REMARK 470 ILE A 115 CD1 REMARK 470 ILE A 119 CD1 REMARK 470 ARG A 122 CG CD NE CZ NH1 NH2 REMARK 470 VAL A 123 CG1 CG2 REMARK 470 MET A 126 CG SD CE REMARK 470 LYS A 128 CG CD CE NZ REMARK 470 TYR A 134 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 GLN A 137 CG CD OE1 NE2 REMARK 470 VAL A 139 CG1 CG2 REMARK 470 GLU A 140 CG CD OE1 OE2 REMARK 470 GLN A 145 CD OE1 NE2 REMARK 470 LYS A 147 CG CD CE NZ REMARK 470 VAL A 149 CG1 CG2 REMARK 470 LEU A 150 CG CD1 CD2 REMARK 470 LEU A 151 CG CD1 CD2 REMARK 470 LEU A 153 CD1 CD2 REMARK 470 LEU A 166 CG CD1 CD2 REMARK 470 ASP A 167 OD1 OD2 REMARK 470 GLU A 171 CD OE1 OE2 REMARK 470 ARG A 175 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 177 CG CD CE NZ REMARK 470 ARG A 197 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 211 CD1 CD2 REMARK 470 LEU A 219 CG CD1 CD2 REMARK 470 LYS A 225 CG CD CE NZ REMARK 470 LYS A 227 CE NZ REMARK 470 LYS A 228 CG CD CE NZ REMARK 470 LYS A 229 CE NZ REMARK 470 LYS A 234 CG CD CE NZ REMARK 470 LYS A 236 CD CE NZ REMARK 470 LYS A 245 CG CD CE NZ REMARK 470 GLN A 256 CG CD OE1 NE2 REMARK 470 MET A 259 SD CE REMARK 470 LEU A 276 CG CD1 CD2 REMARK 470 GLU A 281 CG CD OE1 OE2 REMARK 470 LEU A 284 CG CD1 CD2 REMARK 470 GLU A 285 CG CD OE1 OE2 REMARK 470 ARG A 289 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 292 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 298 CG CD1 CD2 REMARK 470 LEU A 302 CG CD1 CD2 REMARK 470 LEU A 305 CG CD1 CD2 REMARK 470 LEU A 307 CG CD1 CD2 REMARK 470 GLN A 308 CD OE1 NE2 REMARK 470 LEU A 309 CD1 CD2 REMARK 470 PHE A 310 CG CD1 CD2 CE1 CE2 CZ REMARK 470 VAL A 311 CG1 CG2 REMARK 470 LYS A 312 CG CD CE NZ REMARK 470 LEU A 316 CG CD1 CD2 REMARK 470 ARG A 317 CD NE CZ NH1 NH2 REMARK 470 VAL A 324 CG1 CG2 REMARK 470 VAL A 326 CG1 CG2 REMARK 470 ARG A 333 CG CD NE CZ NH1 NH2 REMARK 470 ASP A 341 CG OD1 OD2 REMARK 470 HIS A 342 CG ND1 CD2 CE1 NE2 REMARK 470 PHE A 343 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ASP A 344 CG OD1 OD2 REMARK 470 ILE A 345 CD1 REMARK 470 GLU A 346 CG CD OE1 OE2 REMARK 470 MET A 348 SD CE REMARK 470 LEU A 351 CG CD1 CD2 REMARK 470 LYS A 357 CD CE NZ REMARK 470 LEU A 359 CG CD1 CD2 REMARK 470 ARG A 360 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 363 CG CD1 CD2 REMARK 470 ARG A 370 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 378 CD OE1 OE2 REMARK 470 LEU A 380 CG CD1 CD2 REMARK 470 ARG A 381 CG CD NE CZ NH1 NH2 REMARK 470 LEU A 384 CG CD1 CD2 REMARK 470 CYS A 387 SG REMARK 470 LYS A 389 CA C O CB CG CD CE REMARK 470 LYS A 389 NZ 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 O ALA A 295 ND1 HIS A 299 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OE1 GLU A 87 OG SER A 239 8554 2.11 REMARK 500 CB GLN A 137 CB GLN A 137 7555 2.11 REMARK 500 OH TYR A 260 O3P PLP A 401 8554 2.12 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 371 CD GLU A 371 OE2 0.073 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 GLN A 69 72.56 56.38 REMARK 500 ASP A 98 150.66 -36.00 REMARK 500 HIS A 133 -157.61 -122.08 REMARK 500 HIS A 155 -76.62 -60.41 REMARK 500 ASP A 167 128.35 -38.93 REMARK 500 LYS A 177 -3.52 81.60 REMARK 500 LYS A 209 -110.03 -101.06 REMARK 500 SER A 232 43.20 -145.17 REMARK 500 HIS A 261 -76.13 -107.96 REMARK 500 ARG A 381 -70.28 -53.50 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PLP A 401 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6RV0 RELATED DB: PDB DBREF 6RV1 A 1 392 UNP P21549 SPYA_HUMAN 1 392 SEQRES 1 A 392 MET ALA SER HIS LYS LEU LEU VAL THR PRO PRO LYS ALA SEQRES 2 A 392 LEU LEU LYS PRO LEU SER ILE PRO ASN GLN LEU LEU LEU SEQRES 3 A 392 GLY PRO GLY PRO SER ASN LEU PRO PRO ARG ILE MET ALA SEQRES 4 A 392 ALA GLY GLY LEU GLN MET ILE GLY SER MET SER LYS ASP SEQRES 5 A 392 MET TYR GLN ILE MET ASP GLU ILE LYS GLU GLY ILE GLN SEQRES 6 A 392 TYR VAL PHE GLN THR ARG ASN PRO LEU THR LEU VAL ILE SEQRES 7 A 392 SER GLY SER GLY HIS CYS ALA LEU GLU ALA ALA LEU VAL SEQRES 8 A 392 ASN VAL LEU GLU PRO GLY ASP SER PHE LEU VAL GLY ALA SEQRES 9 A 392 ASN GLY ILE TRP GLY GLN ARG ALA VAL ASP ILE GLY GLU SEQRES 10 A 392 ARG ILE GLY ALA ARG VAL HIS PRO MET THR LYS ASP PRO SEQRES 11 A 392 GLY GLY HIS TYR THR LEU GLN GLU VAL GLU GLU GLY LEU SEQRES 12 A 392 ALA GLN HIS LYS PRO VAL LEU LEU PHE LEU THR HIS GLY SEQRES 13 A 392 GLU SER SER THR GLY VAL LEU GLN PRO LEU ASP GLY PHE SEQRES 14 A 392 GLY GLU LEU CYS HIS ARG TYR LYS CYS LEU LEU LEU VAL SEQRES 15 A 392 ASP SER VAL ALA SER LEU GLY GLY THR PRO LEU TYR MET SEQRES 16 A 392 ASP ARG GLN GLY ILE ASP ILE LEU TYR SER GLY SER GLN SEQRES 17 A 392 LYS ALA LEU ASN ALA PRO PRO GLY THR SER LEU ILE SER SEQRES 18 A 392 PHE SER ASP LYS ALA LYS LYS LYS MET TYR SER ARG LYS SEQRES 19 A 392 THR LYS PRO PHE SER PHE TYR LEU ASP ILE LYS TRP LEU SEQRES 20 A 392 ALA ASN PHE TRP GLY CYS ASP ASP GLN PRO ARG MET TYR SEQRES 21 A 392 HIS HIS THR ILE PRO VAL ILE SER LEU TYR SER LEU ARG SEQRES 22 A 392 GLU SER LEU ALA LEU ILE ALA GLU GLN GLY LEU GLU ASN SEQRES 23 A 392 SER TRP ARG GLN HIS ARG GLU ALA ALA ALA TYR LEU HIS SEQRES 24 A 392 GLY ARG LEU GLN ALA LEU GLY LEU GLN LEU PHE VAL LYS SEQRES 25 A 392 ASP PRO ALA LEU ARG LEU PRO THR VAL THR THR VAL ALA SEQRES 26 A 392 VAL PRO ALA GLY TYR ASP TRP ARG ASP ILE VAL SER TYR SEQRES 27 A 392 VAL ILE ASP HIS PHE ASP ILE GLU ILE MET GLY GLY LEU SEQRES 28 A 392 GLY PRO SER THR GLY LYS VAL LEU ARG ILE GLY LEU LEU SEQRES 29 A 392 GLY CYS ASN ALA THR ARG GLU ASN VAL ASP ARG VAL THR SEQRES 30 A 392 GLU ALA LEU ARG ALA ALA LEU GLN HIS CYS PRO LYS LYS SEQRES 31 A 392 LYS LEU HET PLP A 401 15 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 2 PLP C8 H10 N O6 P FORMUL 3 HOH *2(H2 O) HELIX 1 AA1 PRO A 11 LYS A 16 5 6 HELIX 2 AA2 PRO A 34 GLY A 42 1 9 HELIX 3 AA3 SER A 50 GLN A 69 1 20 HELIX 4 AA4 SER A 81 LEU A 94 1 14 HELIX 5 AA5 GLY A 106 GLY A 106 1 1 HELIX 6 AA6 TRP A 108 ILE A 119 1 12 HELIX 7 AA7 THR A 135 LYS A 147 1 13 HELIX 8 AA8 GLY A 168 TYR A 176 1 9 HELIX 9 AA9 MET A 195 GLY A 199 5 5 HELIX 10 AB1 SER A 223 TYR A 231 1 9 HELIX 11 AB2 ASP A 243 TRP A 251 1 9 HELIX 12 AB3 PRO A 265 GLY A 283 1 19 HELIX 13 AB4 GLY A 283 GLY A 306 1 24 HELIX 14 AB5 ASP A 313 ARG A 317 5 5 HELIX 15 AB6 ASP A 331 ASP A 344 1 14 HELIX 16 AB7 LEU A 364 ALA A 368 5 5 HELIX 17 AB8 THR A 369 GLN A 385 1 17 SHEET 1 AA1 2 LEU A 24 LEU A 25 0 SHEET 2 AA1 2 ILE A 345 GLU A 346 1 O GLU A 346 N LEU A 24 SHEET 1 AA2 7 LEU A 74 ILE A 78 0 SHEET 2 AA2 7 SER A 218 PHE A 222 -1 O PHE A 222 N LEU A 74 SHEET 3 AA2 7 ILE A 202 GLY A 206 -1 N SER A 205 O LEU A 219 SHEET 4 AA2 7 LEU A 179 ASP A 183 1 N LEU A 180 O ILE A 202 SHEET 5 AA2 7 LEU A 150 THR A 154 1 N LEU A 151 O LEU A 181 SHEET 6 AA2 7 GLY A 97 VAL A 102 1 N LEU A 101 O LEU A 150 SHEET 7 AA2 7 ALA A 121 PRO A 125 1 O ARG A 122 N ASP A 98 SHEET 1 AA3 2 VAL A 321 ALA A 325 0 SHEET 2 AA3 2 VAL A 358 GLY A 362 -1 O LEU A 359 N VAL A 324 LINK NZ LYS A 209 C4A PLP A 401 1555 1555 1.29 CISPEP 1 GLY A 29 PRO A 30 0 -11.23 SITE 1 AC1 14 SER A 81 GLY A 82 HIS A 83 TRP A 108 SITE 2 AC1 14 GLY A 156 SER A 158 ASP A 183 VAL A 185 SITE 3 AC1 14 ALA A 186 GLN A 208 LYS A 209 TYR A 260 SITE 4 AC1 14 HIS A 262 THR A 263 CRYST1 89.333 89.333 140.797 90.00 90.00 90.00 P 41 21 2 8 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 0.011194 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011194 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007102 0.00000