HEADER TRANSFERASE 10-DEC-15 5F9S TITLE CRYSTAL STRUCTURE OF HUMAN ALANINE:GLYOXYLATE AMINOTRANSFERASE MAJOR TITLE 2 ALLELE (AGT-MA) AT 1.7 ANGSTROM; INTERNAL ALDIMINE WITH PLP IN THE TITLE 3 ACTIVE SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: SERINE--PYRUVATE AMINOTRANSFERASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: ALANINE:GLYOXYLATE AMINOTRANSFERASE MAJOR ALLELE (AGT-MA), COMPND 5 SPT,ALANINE--GLYOXYLATE AMINOTRANSFERASE,AGT; COMPND 6 EC: 2.6.1.51,2.6.1.44; COMPND 7 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; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: JM109; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PTRCHIS2A KEYWDS AMINOTRANSFERASE, DETOXIFICATION, LIVER, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR G.GIARDINA,F.CUTRUZZOLA,C.BORRI VOLTATTORNI,B.CELLINI,R.MONTIOLI REVDAT 3 10-JAN-24 5F9S 1 REMARK REVDAT 2 27-SEP-17 5F9S 1 JRNL REMARK REVDAT 1 21-DEC-16 5F9S 0 JRNL AUTH G.GIARDINA,A.PAIARDINI,R.MONTIOLI,B.CELLINI,C.B.VOLTATTORNI, JRNL AUTH 2 F.CUTRUZZOLA JRNL TITL RADIATION DAMAGE AT THE ACTIVE SITE OF HUMAN JRNL TITL 2 ALANINE:GLYOXYLATE AMINOTRANSFERASE REVEALS THAT THE JRNL TITL 3 COFACTOR POSITION IS FINELY TUNED DURING CATALYSIS. JRNL REF SCI REP V. 7 11704 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 28916765 JRNL DOI 10.1038/S41598-017-11948-W REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.10.1 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.12 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 86.3 REMARK 3 NUMBER OF REFLECTIONS : 70010 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.870 REMARK 3 FREE R VALUE TEST SET COUNT : 3411 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 45.1339 - 4.9017 0.83 2889 151 0.1446 0.1604 REMARK 3 2 4.9017 - 3.8913 0.85 2805 135 0.1194 0.1457 REMARK 3 3 3.8913 - 3.3996 0.86 2826 132 0.1299 0.1704 REMARK 3 4 3.3996 - 3.0888 0.86 2824 148 0.1432 0.1784 REMARK 3 5 3.0888 - 2.8675 0.86 2788 125 0.1485 0.2011 REMARK 3 6 2.8675 - 2.6984 0.87 2836 138 0.1471 0.1981 REMARK 3 7 2.6984 - 2.5633 0.87 2788 157 0.1530 0.1882 REMARK 3 8 2.5633 - 2.4517 0.88 2832 147 0.1498 0.1937 REMARK 3 9 2.4517 - 2.3574 0.88 2842 128 0.1523 0.2271 REMARK 3 10 2.3574 - 2.2760 0.89 2820 174 0.1587 0.2193 REMARK 3 11 2.2760 - 2.2049 0.88 2869 116 0.1605 0.2367 REMARK 3 12 2.2049 - 2.1418 0.88 2806 144 0.1742 0.2248 REMARK 3 13 2.1418 - 2.0854 0.87 2783 150 0.1854 0.2484 REMARK 3 14 2.0854 - 2.0346 0.87 2776 154 0.1878 0.2466 REMARK 3 15 2.0346 - 1.9883 0.87 2754 152 0.1930 0.2625 REMARK 3 16 1.9883 - 1.9460 0.87 2791 137 0.1981 0.2698 REMARK 3 17 1.9460 - 1.9071 0.86 2773 143 0.2090 0.2575 REMARK 3 18 1.9071 - 1.8711 0.87 2710 153 0.2121 0.2624 REMARK 3 19 1.8711 - 1.8377 0.86 2747 131 0.2141 0.2619 REMARK 3 20 1.8377 - 1.8065 0.85 2683 146 0.2264 0.2752 REMARK 3 21 1.8065 - 1.7774 0.85 2720 124 0.2236 0.3240 REMARK 3 22 1.7774 - 1.7500 0.85 2700 130 0.2393 0.2978 REMARK 3 23 1.7500 - 1.7243 0.83 2663 139 0.2250 0.2771 REMARK 3 24 1.7243 - 1.7000 0.83 2574 157 0.2344 0.2996 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.270 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.08 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.011 6252 REMARK 3 ANGLE : 1.150 8511 REMARK 3 CHIRALITY : 0.056 945 REMARK 3 PLANARITY : 0.007 1098 REMARK 3 DIHEDRAL : 14.617 3803 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5F9S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-DEC-15. REMARK 100 THE DEPOSITION ID IS D_1000215218. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAR-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5-6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS 0.3.11 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70070 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 48.040 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.0 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.4 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.61400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 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: 1HOC REMARK 200 REMARK 200 REMARK: YELLOW PLATES REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.14 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN SOLUTION; 0.2 M AGT, 18MM REMARK 280 POTASSIUM PHOSPHATE PH7.4, 20MM HEPES PH 7.4, 5% JEFFAMINE REMARK 280 (HAMPTON), 5MM SODIUM HYDROXYLAMINE. RESERVOIR; PEG 6K 12%, 100 REMARK 280 MM MES PH 5.0. MIXING: 1+1 MICROL CRYOPROTECTANT; 25% MPD, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-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 -1.000000 0.000000 0.000000 27.23950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 65.66900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 50.94000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 65.66900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 27.23950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 50.94000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 8930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26230 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -55.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 LYS A 391 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 12 CD CE NZ REMARK 480 LYS A 16 CD CE NZ REMARK 480 LYS A 51 CG CD CE NZ REMARK 480 LYS A 147 CE NZ REMARK 480 GLU A 171 CD OE1 OE2 REMARK 480 LYS A 177 CD CE NZ REMARK 480 LYS A 228 CD CE NZ REMARK 480 LYS A 234 CD CE NZ REMARK 480 LYS A 312 CD CE NZ REMARK 480 GLU A 371 CD OE1 OE2 REMARK 480 ARG A 375 NE CZ NH1 NH2 REMARK 480 LYS B 16 CG CD CE NZ REMARK 480 LYS B 51 CG CD CE NZ REMARK 480 ARG B 71 CD NE CZ NH1 NH2 REMARK 480 LYS B 147 CD CE NZ REMARK 480 GLU B 171 CG CD OE1 OE2 REMARK 480 LYS B 177 CE NZ REMARK 480 LYS B 234 CG CD CE NZ REMARK 480 ARG B 289 NE CZ NH1 NH2 REMARK 480 ARG B 375 NE CZ NH1 NH2 REMARK 480 GLN B 385 CD OE1 NE2 REMARK 480 LYS B 390 CG CD CE 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 B 144 HZ3 LYS B 147 1.14 REMARK 500 HH11 ARG B 71 O HOH B 506 1.31 REMARK 500 HH21 ARG B 122 O HOH B 504 1.36 REMARK 500 HH21 ARG B 122 O HOH B 502 1.39 REMARK 500 HG CYS B 366 O HOH B 815 1.40 REMARK 500 HH22 ARG B 301 O HOH B 507 1.47 REMARK 500 HE ARG A 71 O HOH A 509 1.52 REMARK 500 O HIS B 174 HZ2 LYS B 177 1.57 REMARK 500 HD1 HIS A 299 O HOH A 513 1.58 REMARK 500 O ALA B 144 NZ LYS B 147 1.70 REMARK 500 O HOH A 762 O HOH B 827 1.76 REMARK 500 OE2 GLU A 371 O HOH A 501 1.80 REMARK 500 O HOH B 782 O HOH B 848 2.01 REMARK 500 O HOH A 585 O HOH A 763 2.02 REMARK 500 O ALA B 328 O HOH B 501 2.04 REMARK 500 O HOH A 569 O HOH A 851 2.05 REMARK 500 NH2 ARG B 122 O HOH B 502 2.05 REMARK 500 O HIS B 174 NZ LYS B 177 2.08 REMARK 500 O HOH A 563 O HOH A 779 2.09 REMARK 500 NH2 ARG B 122 O HOH B 504 2.11 REMARK 500 O HIS B 386 O HOH B 505 2.12 REMARK 500 NH1 ARG B 71 O HOH B 506 2.12 REMARK 500 NH2 ARG A 375 O HOH A 502 2.13 REMARK 500 OE1 GLN A 110 O HOH A 503 2.13 REMARK 500 OD1 ASN A 367 O HOH A 504 2.15 REMARK 500 O HOH B 748 O HOH B 837 2.16 REMARK 500 O HOH B 516 O HOH B 774 2.16 REMARK 500 O HOH B 805 O HOH B 834 2.16 REMARK 500 NH2 ARG A 122 O HOH A 505 2.18 REMARK 500 O HOH A 545 O HOH A 886 2.18 REMARK 500 O HOH A 707 O HOH A 889 2.19 REMARK 500 O HOH A 585 O HOH A 811 2.19 REMARK 500 O HOH A 811 O HOH A 909 2.19 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 HG CYS B 366 O HOH B 828 3655 1.12 REMARK 500 HZ1 LYS A 177 O PHE B 343 3545 1.41 REMARK 500 NZ LYS A 177 O PHE B 343 3545 2.00 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 LYS A 177 CE LYS A 177 NZ -0.209 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 122 NE - CZ - NH2 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 375 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 MET B 45 CG - SD - CE ANGL. DEV. = -10.1 DEGREES REMARK 500 ARG B 197 NE - CZ - NH1 ANGL. DEV. = 3.8 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 GLN A 69 62.12 61.28 REMARK 500 LYS A 209 -120.91 -95.52 REMARK 500 ASP A 255 39.49 -94.70 REMARK 500 HIS A 261 -70.26 -114.57 REMARK 500 GLN B 69 61.46 60.98 REMARK 500 LYS B 209 -118.80 -94.86 REMARK 500 ASP B 254 -166.15 -126.35 REMARK 500 LYS B 390 150.28 -49.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 917 DISTANCE = 6.13 ANGSTROMS REMARK 525 HOH B 883 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH B 884 DISTANCE = 8.72 ANGSTROMS REMARK 525 HOH B 885 DISTANCE = 9.93 ANGSTROMS 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 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide PLP B 401 and LYS B REMARK 800 209 DBREF 5F9S A 6 391 UNP P21549 SPYA_HUMAN 6 391 DBREF 5F9S B 6 391 UNP P21549 SPYA_HUMAN 6 391 SEQRES 1 A 386 LEU LEU VAL THR PRO PRO LYS ALA LEU LEU LYS PRO LEU SEQRES 2 A 386 SER ILE PRO ASN GLN LEU LEU LEU GLY PRO GLY PRO SER SEQRES 3 A 386 ASN LEU PRO PRO ARG ILE MET ALA ALA GLY GLY LEU GLN SEQRES 4 A 386 MET ILE GLY SER MET SER LYS ASP MET TYR GLN ILE MET SEQRES 5 A 386 ASP GLU ILE LYS GLU GLY ILE GLN TYR VAL PHE GLN THR SEQRES 6 A 386 ARG ASN PRO LEU THR LEU VAL ILE SER GLY SER GLY HIS SEQRES 7 A 386 CYS ALA LEU GLU ALA ALA LEU VAL ASN VAL LEU GLU PRO SEQRES 8 A 386 GLY ASP SER PHE LEU VAL GLY ALA ASN GLY ILE TRP GLY SEQRES 9 A 386 GLN ARG ALA VAL ASP ILE GLY GLU ARG ILE GLY ALA ARG SEQRES 10 A 386 VAL HIS PRO MET THR LYS ASP PRO GLY GLY HIS TYR THR SEQRES 11 A 386 LEU GLN GLU VAL GLU GLU GLY LEU ALA GLN HIS LYS PRO SEQRES 12 A 386 VAL LEU LEU PHE LEU THR HIS GLY GLU SER SER THR GLY SEQRES 13 A 386 VAL LEU GLN PRO LEU ASP GLY PHE GLY GLU LEU CYS HIS SEQRES 14 A 386 ARG TYR LYS CYS LEU LEU LEU VAL ASP SER VAL ALA SER SEQRES 15 A 386 LEU GLY GLY THR PRO LEU TYR MET ASP ARG GLN GLY ILE SEQRES 16 A 386 ASP ILE LEU TYR SER GLY SER GLN LYS ALA LEU ASN ALA SEQRES 17 A 386 PRO PRO GLY THR SER LEU ILE SER PHE SER ASP LYS ALA SEQRES 18 A 386 LYS LYS LYS MET TYR SER ARG LYS THR LYS PRO PHE SER SEQRES 19 A 386 PHE TYR LEU ASP ILE LYS TRP LEU ALA ASN PHE TRP GLY SEQRES 20 A 386 CYS ASP ASP GLN PRO ARG MET TYR HIS HIS THR ILE PRO SEQRES 21 A 386 VAL ILE SER LEU TYR SER LEU ARG GLU SER LEU ALA LEU SEQRES 22 A 386 ILE ALA GLU GLN GLY LEU GLU ASN SER TRP ARG GLN HIS SEQRES 23 A 386 ARG GLU ALA ALA ALA TYR LEU HIS GLY ARG LEU GLN ALA SEQRES 24 A 386 LEU GLY LEU GLN LEU PHE VAL LYS ASP PRO ALA LEU ARG SEQRES 25 A 386 LEU PRO THR VAL THR THR VAL ALA VAL PRO ALA GLY TYR SEQRES 26 A 386 ASP TRP ARG ASP ILE VAL SER TYR VAL ILE ASP HIS PHE SEQRES 27 A 386 ASP ILE GLU ILE MET GLY GLY LEU GLY PRO SER THR GLY SEQRES 28 A 386 LYS VAL LEU ARG ILE GLY LEU LEU GLY CYS ASN ALA THR SEQRES 29 A 386 ARG GLU ASN VAL ASP ARG VAL THR GLU ALA LEU ARG ALA SEQRES 30 A 386 ALA LEU GLN HIS CYS PRO LYS LYS LYS SEQRES 1 B 386 LEU LEU VAL THR PRO PRO LYS ALA LEU LEU LYS PRO LEU SEQRES 2 B 386 SER ILE PRO ASN GLN LEU LEU LEU GLY PRO GLY PRO SER SEQRES 3 B 386 ASN LEU PRO PRO ARG ILE MET ALA ALA GLY GLY LEU GLN SEQRES 4 B 386 MET ILE GLY SER MET SER LYS ASP MET TYR GLN ILE MET SEQRES 5 B 386 ASP GLU ILE LYS GLU GLY ILE GLN TYR VAL PHE GLN THR SEQRES 6 B 386 ARG ASN PRO LEU THR LEU VAL ILE SER GLY SER GLY HIS SEQRES 7 B 386 CYS ALA LEU GLU ALA ALA LEU VAL ASN VAL LEU GLU PRO SEQRES 8 B 386 GLY ASP SER PHE LEU VAL GLY ALA ASN GLY ILE TRP GLY SEQRES 9 B 386 GLN ARG ALA VAL ASP ILE GLY GLU ARG ILE GLY ALA ARG SEQRES 10 B 386 VAL HIS PRO MET THR LYS ASP PRO GLY GLY HIS TYR THR SEQRES 11 B 386 LEU GLN GLU VAL GLU GLU GLY LEU ALA GLN HIS LYS PRO SEQRES 12 B 386 VAL LEU LEU PHE LEU THR HIS GLY GLU SER SER THR GLY SEQRES 13 B 386 VAL LEU GLN PRO LEU ASP GLY PHE GLY GLU LEU CYS HIS SEQRES 14 B 386 ARG TYR LYS CYS LEU LEU LEU VAL ASP SER VAL ALA SER SEQRES 15 B 386 LEU GLY GLY THR PRO LEU TYR MET ASP ARG GLN GLY ILE SEQRES 16 B 386 ASP ILE LEU TYR SER GLY SER GLN LYS ALA LEU ASN ALA SEQRES 17 B 386 PRO PRO GLY THR SER LEU ILE SER PHE SER ASP LYS ALA SEQRES 18 B 386 LYS LYS LYS MET TYR SER ARG LYS THR LYS PRO PHE SER SEQRES 19 B 386 PHE TYR LEU ASP ILE LYS TRP LEU ALA ASN PHE TRP GLY SEQRES 20 B 386 CYS ASP ASP GLN PRO ARG MET TYR HIS HIS THR ILE PRO SEQRES 21 B 386 VAL ILE SER LEU TYR SER LEU ARG GLU SER LEU ALA LEU SEQRES 22 B 386 ILE ALA GLU GLN GLY LEU GLU ASN SER TRP ARG GLN HIS SEQRES 23 B 386 ARG GLU ALA ALA ALA TYR LEU HIS GLY ARG LEU GLN ALA SEQRES 24 B 386 LEU GLY LEU GLN LEU PHE VAL LYS ASP PRO ALA LEU ARG SEQRES 25 B 386 LEU PRO THR VAL THR THR VAL ALA VAL PRO ALA GLY TYR SEQRES 26 B 386 ASP TRP ARG ASP ILE VAL SER TYR VAL ILE ASP HIS PHE SEQRES 27 B 386 ASP ILE GLU ILE MET GLY GLY LEU GLY PRO SER THR GLY SEQRES 28 B 386 LYS VAL LEU ARG ILE GLY LEU LEU GLY CYS ASN ALA THR SEQRES 29 B 386 ARG GLU ASN VAL ASP ARG VAL THR GLU ALA LEU ARG ALA SEQRES 30 B 386 ALA LEU GLN HIS CYS PRO LYS LYS LYS HET PLP A 401 24 HET PLP B 401 24 HETNAM PLP PYRIDOXAL-5'-PHOSPHATE HETSYN PLP VITAMIN B6 PHOSPHATE FORMUL 3 PLP 2(C8 H10 N O6 P) FORMUL 5 HOH *802(H2 O) HELIX 1 AA1 LYS A 12 LYS A 16 5 5 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 ILE A 119 1 14 HELIX 6 AA6 THR A 135 LYS A 147 1 13 HELIX 7 AA7 GLY A 168 TYR A 176 1 9 HELIX 8 AA8 SER A 223 SER A 232 1 10 HELIX 9 AA9 ASP A 243 TRP A 251 1 9 HELIX 10 AB1 PRO A 265 GLY A 283 1 19 HELIX 11 AB2 GLY A 283 LEU A 305 1 23 HELIX 12 AB3 ASP A 313 ARG A 317 5 5 HELIX 13 AB4 ASP A 331 ASP A 344 1 14 HELIX 14 AB5 LEU A 351 THR A 355 5 5 HELIX 15 AB6 LEU A 364 ALA A 368 5 5 HELIX 16 AB7 THR A 369 CYS A 387 1 19 HELIX 17 AB8 PRO B 11 LYS B 16 5 6 HELIX 18 AB9 PRO B 34 GLY B 42 1 9 HELIX 19 AC1 SER B 50 GLN B 69 1 20 HELIX 20 AC2 SER B 81 LEU B 94 1 14 HELIX 21 AC3 GLY B 106 ILE B 119 1 14 HELIX 22 AC4 THR B 135 LYS B 147 1 13 HELIX 23 AC5 GLY B 168 TYR B 176 1 9 HELIX 24 AC6 SER B 223 ARG B 233 1 11 HELIX 25 AC7 ASP B 243 TRP B 251 1 9 HELIX 26 AC8 PRO B 265 GLY B 283 1 19 HELIX 27 AC9 GLY B 283 LEU B 305 1 23 HELIX 28 AD1 ASP B 313 ARG B 317 5 5 HELIX 29 AD2 ASP B 331 ASP B 344 1 14 HELIX 30 AD3 LEU B 351 THR B 355 5 5 HELIX 31 AD4 LEU B 364 ALA B 368 5 5 HELIX 32 AD5 THR B 369 CYS B 387 1 19 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 SER A 218 N ILE A 78 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 VAL A 182 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 SER A 99 ALA A 104 1 N LEU A 101 O LEU A 150 SHEET 7 AA2 7 ARG A 122 THR A 127 1 O MET A 126 N VAL A 102 SHEET 1 AA3 3 GLN A 308 LEU A 309 0 SHEET 2 AA3 3 VAL A 321 ALA A 325 -1 O ALA A 325 N GLN A 308 SHEET 3 AA3 3 VAL A 358 GLY A 362 -1 O ILE A 361 N THR A 322 SHEET 1 AA4 2 LEU B 24 LEU B 25 0 SHEET 2 AA4 2 ILE B 345 GLU B 346 1 O GLU B 346 N LEU B 24 SHEET 1 AA5 7 LEU B 74 ILE B 78 0 SHEET 2 AA5 7 SER B 218 PHE B 222 -1 O SER B 218 N ILE B 78 SHEET 3 AA5 7 ILE B 202 GLY B 206 -1 N SER B 205 O LEU B 219 SHEET 4 AA5 7 LEU B 179 ASP B 183 1 N VAL B 182 O ILE B 202 SHEET 5 AA5 7 LEU B 150 THR B 154 1 N LEU B 151 O LEU B 181 SHEET 6 AA5 7 SER B 99 ALA B 104 1 N GLY B 103 O PHE B 152 SHEET 7 AA5 7 ARG B 122 THR B 127 1 O MET B 126 N VAL B 102 SHEET 1 AA6 2 VAL B 321 ALA B 325 0 SHEET 2 AA6 2 VAL B 358 GLY B 362 -1 O ILE B 361 N THR B 322 LINK NZ LYS A 209 C4A PLP A 401 1555 1555 1.47 LINK NZ LYS B 209 C4A PLP B 401 1555 1555 1.46 CISPEP 1 GLY A 29 PRO A 30 0 -10.59 CISPEP 2 GLY B 29 PRO B 30 0 -0.61 SITE 1 AC1 13 SER A 81 GLY A 82 HIS A 83 TRP A 108 SITE 2 AC1 13 GLY A 156 SER A 158 ASP A 183 VAL A 185 SITE 3 AC1 13 ALA A 186 GLN A 208 LYS A 209 TYR B 260 SITE 4 AC1 13 THR B 263 SITE 1 AC2 21 TYR A 260 THR A 263 PRO B 28 SER B 31 SITE 2 AC2 21 SER B 81 GLY B 82 HIS B 83 TRP B 108 SITE 3 AC2 21 GLY B 156 SER B 158 ASP B 183 VAL B 185 SITE 4 AC2 21 ALA B 186 SER B 207 GLN B 208 ALA B 210 SITE 5 AC2 21 LEU B 211 ASN B 212 LEU B 364 HOH B 634 SITE 6 AC2 21 HOH B 648 CRYST1 54.479 101.880 131.338 90.00 90.00 90.00 P 21 21 21 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 0.018356 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009815 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007614 0.00000