HEADER LYASE 31-MAY-22 8D2Y TITLE Y430F MUTANT OF D-ORNITHINE/D-LYSINE DECARBOXYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-ORNITHINE/D-LYSINE DECARBOXYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: D-ORN/D-LYS DECARBOXYLASE,DOKDC; COMPND 5 EC: 4.1.1.116; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SALMONELLA ENTERICA SUBSP. ENTERICA SEROVAR SOURCE 3 TYPHIMURIUM; SOURCE 4 ORGANISM_TAXID: 90371; SOURCE 5 STRAIN: LT2 / SGSC1412 / ATCC 700720; SOURCE 6 GENE: DOKD, STM2360; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS PYRIDOXAL-5'-PHOSPHATE, DECARBOXYLASE, D-AMINO ACID, FOLD III, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR R.S.PHILLIPS,K.N.NGUYEN HOANG REVDAT 3 15-NOV-23 8D2Y 1 REMARK REVDAT 2 18-OCT-23 8D2Y 1 REMARK REVDAT 1 16-NOV-22 8D2Y 0 JRNL AUTH R.S.PHILLIPS,K.N.NGUYEN HOANG JRNL TITL THE Y430F MUTANT OF SALMONELLA D-ORNITHINE/D-LYSINE JRNL TITL 2 DECARBOXYLASE HAS ALTERED STEREOSPECIFICITY AND A PUTRESCINE JRNL TITL 3 ALLOSTERIC ACTIVATION SITE. JRNL REF ARCH.BIOCHEM.BIOPHYS. V. 731 09429 2022 JRNL REFN ESSN 1096-0384 JRNL PMID 36265649 JRNL DOI 10.1016/J.ABB.2022.109429 REMARK 2 REMARK 2 RESOLUTION. 1.22 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.22 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.66 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 77.9 REMARK 3 NUMBER OF REFLECTIONS : 101767 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.134 REMARK 3 R VALUE (WORKING SET) : 0.134 REMARK 3 FREE R VALUE : 0.152 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 1.970 REMARK 3 FREE R VALUE TEST SET COUNT : 2002 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 36.6600 - 2.9400 1.00 9385 188 0.1171 0.1202 REMARK 3 2 2.9400 - 2.3400 1.00 9202 188 0.1208 0.1356 REMARK 3 3 2.3400 - 2.0400 1.00 9174 176 0.1203 0.1645 REMARK 3 4 2.0400 - 1.8500 1.00 9162 184 0.1292 0.1470 REMARK 3 5 1.8500 - 1.7200 1.00 9140 181 0.1362 0.1649 REMARK 3 6 1.7200 - 1.6200 1.00 9121 188 0.1452 0.1984 REMARK 3 7 1.6200 - 1.5400 1.00 9100 181 0.1453 0.1672 REMARK 3 8 1.5400 - 1.4700 0.99 9120 182 0.1619 0.1856 REMARK 3 9 1.4700 - 1.4200 0.96 8694 177 0.1967 0.2255 REMARK 3 10 1.4200 - 1.3700 0.86 7864 157 0.2337 0.2474 REMARK 3 11 1.3700 - 1.3200 0.64 5839 117 0.2819 0.3021 REMARK 3 12 1.3200 - 1.2900 0.30 2741 59 0.3169 0.3375 REMARK 3 13 1.2900 - 1.2500 0.10 932 18 0.2853 0.3047 REMARK 3 14 1.2500 - 1.2200 0.03 291 6 0.3767 0.3186 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.102 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.193 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.22 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 : 0.008 4280 REMARK 3 ANGLE : 1.145 5851 REMARK 3 CHIRALITY : 0.088 620 REMARK 3 PLANARITY : 0.013 778 REMARK 3 DIHEDRAL : 13.718 1677 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 7 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 1 THROUGH 94 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.7037 -5.1983 22.9775 REMARK 3 T TENSOR REMARK 3 T11: 0.1148 T22: 0.3303 REMARK 3 T33: 0.0832 T12: -0.0250 REMARK 3 T13: 0.0134 T23: 0.0318 REMARK 3 L TENSOR REMARK 3 L11: 0.7882 L22: 0.5009 REMARK 3 L33: 0.6404 L12: -0.1429 REMARK 3 L13: 0.2374 L23: -0.0730 REMARK 3 S TENSOR REMARK 3 S11: -0.0014 S12: -0.4995 S13: -0.0565 REMARK 3 S21: 0.0651 S22: 0.0097 S23: 0.0479 REMARK 3 S31: -0.0009 S32: -0.2603 S33: -0.0331 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 95 THROUGH 183 ) REMARK 3 ORIGIN FOR THE GROUP (A): 22.3695 1.4807 10.7389 REMARK 3 T TENSOR REMARK 3 T11: 0.0973 T22: 0.1152 REMARK 3 T33: 0.0769 T12: -0.0363 REMARK 3 T13: -0.0072 T23: 0.0085 REMARK 3 L TENSOR REMARK 3 L11: 2.3782 L22: 0.6068 REMARK 3 L33: 1.7392 L12: -0.1910 REMARK 3 L13: 0.1813 L23: -0.1108 REMARK 3 S TENSOR REMARK 3 S11: -0.0270 S12: 0.0059 S13: 0.0652 REMARK 3 S21: 0.0186 S22: -0.0324 S23: -0.0426 REMARK 3 S31: -0.1095 S32: 0.1260 S33: 0.0246 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 184 THROUGH 206 ) REMARK 3 ORIGIN FOR THE GROUP (A): 30.9064 -13.6049 8.6039 REMARK 3 T TENSOR REMARK 3 T11: 0.1448 T22: 0.2094 REMARK 3 T33: 0.1550 T12: 0.0418 REMARK 3 T13: 0.0257 T23: 0.0079 REMARK 3 L TENSOR REMARK 3 L11: 4.2123 L22: 1.4915 REMARK 3 L33: 2.5702 L12: -1.1520 REMARK 3 L13: 0.7844 L23: -0.5970 REMARK 3 S TENSOR REMARK 3 S11: 0.1851 S12: 0.2627 S13: -0.3850 REMARK 3 S21: -0.1520 S22: -0.1103 S23: -0.1335 REMARK 3 S31: 0.2507 S32: 0.2920 S33: -0.0955 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 207 THROUGH 247 ) REMARK 3 ORIGIN FOR THE GROUP (A): 25.4572 -13.6289 18.6437 REMARK 3 T TENSOR REMARK 3 T11: 0.1041 T22: 0.1630 REMARK 3 T33: 0.1155 T12: -0.0088 REMARK 3 T13: -0.0151 T23: 0.0277 REMARK 3 L TENSOR REMARK 3 L11: 3.0093 L22: 0.7877 REMARK 3 L33: 1.2993 L12: 0.2229 REMARK 3 L13: 0.5585 L23: -0.3289 REMARK 3 S TENSOR REMARK 3 S11: 0.1466 S12: -0.1739 S13: -0.3730 REMARK 3 S21: 0.0725 S22: -0.0580 S23: -0.0197 REMARK 3 S31: 0.1061 S32: 0.0471 S33: -0.0668 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 248 THROUGH 283 ) REMARK 3 ORIGIN FOR THE GROUP (A): 6.8504 -17.8464 20.5877 REMARK 3 T TENSOR REMARK 3 T11: 0.1420 T22: 0.2113 REMARK 3 T33: 0.2386 T12: -0.0492 REMARK 3 T13: -0.0475 T23: 0.1222 REMARK 3 L TENSOR REMARK 3 L11: 1.0666 L22: 0.7199 REMARK 3 L33: 0.6605 L12: 0.2817 REMARK 3 L13: -0.4431 L23: -0.3624 REMARK 3 S TENSOR REMARK 3 S11: 0.2427 S12: -0.4826 S13: -0.6305 REMARK 3 S21: 0.0750 S22: -0.0846 S23: -0.0318 REMARK 3 S31: 0.1503 S32: -0.1532 S33: -0.0844 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 284 THROUGH 446 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.9388 -10.9326 11.2528 REMARK 3 T TENSOR REMARK 3 T11: 0.1098 T22: 0.1801 REMARK 3 T33: 0.1208 T12: -0.0201 REMARK 3 T13: 0.0014 T23: 0.0348 REMARK 3 L TENSOR REMARK 3 L11: 1.1409 L22: 0.1541 REMARK 3 L33: 0.5158 L12: 0.0705 REMARK 3 L13: 0.3255 L23: -0.0306 REMARK 3 S TENSOR REMARK 3 S11: 0.0598 S12: -0.2166 S13: -0.1859 REMARK 3 S21: 0.0117 S22: 0.0013 S23: 0.0209 REMARK 3 S31: 0.0454 S32: -0.1545 S33: -0.0579 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 447 THROUGH 468 ) REMARK 3 ORIGIN FOR THE GROUP (A): -4.6012 11.0077 -0.8416 REMARK 3 T TENSOR REMARK 3 T11: 0.1454 T22: 0.1015 REMARK 3 T33: 0.1485 T12: 0.0173 REMARK 3 T13: -0.0172 T23: 0.0073 REMARK 3 L TENSOR REMARK 3 L11: 2.7103 L22: 1.1932 REMARK 3 L33: 2.9210 L12: 0.2246 REMARK 3 L13: -1.5920 L23: 1.3468 REMARK 3 S TENSOR REMARK 3 S11: 0.0288 S12: 0.1494 S13: 0.2910 REMARK 3 S21: -0.1459 S22: 0.0756 S23: 0.0676 REMARK 3 S31: -0.2059 S32: -0.0336 S33: -0.0902 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 8D2Y COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 01-JUN-22. REMARK 100 THE DEPOSITION ID IS D_1000265903. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 27-FEB-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : AUTOPROC REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 101867 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.220 REMARK 200 RESOLUTION RANGE LOW (A) : 36.660 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 77.9 REMARK 200 DATA REDUNDANCY : 13.80 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 17.7800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.22 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.27 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: PHASER REMARK 200 STARTING MODEL: 6N2H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.24 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.13 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, PH 7.5, 0.2-0.4 M NAOAC, REMARK 280 20% PEG 4000, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 69.87000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.37000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 69.87000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.37000 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: 14350 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31030 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -30.0 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 0.00000 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 A 644 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 885 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1024 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1111 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 SER A 176 REMARK 465 ALA A 177 REMARK 465 THR A 178 REMARK 465 HIS A 179 REMARK 465 ALA A 180 REMARK 465 GLU A 181 REMARK 465 LEU A 182 REMARK 465 ALA A 469 REMARK 465 LEU A 470 REMARK 465 GLU A 471 REMARK 465 HIS A 472 REMARK 465 HIS A 473 REMARK 465 HIS A 474 REMARK 465 HIS A 475 REMARK 465 HIS A 476 REMARK 465 HIS A 477 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 O1 EDO A 502 O HOH A 602 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 O HOH A 888 O HOH A 1169 1565 2.16 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 ASN A 72 59.11 -92.33 REMARK 500 CYS A 82 119.49 -174.78 REMARK 500 TRP A 298 -62.64 -109.93 REMARK 500 ASP A 388 118.91 -163.34 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 ARG A 293 0.09 SIDE CHAIN REMARK 500 ARG A 328 0.11 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 K A 512 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE A 204 O REMARK 620 2 LEU A 205 O 71.9 REMARK 620 3 MET A 207 O 86.7 93.3 REMARK 620 4 VAL A 210 O 88.7 160.5 87.7 REMARK 620 5 HOH A 827 O 154.1 84.7 83.8 114.8 REMARK 620 6 HOH A1075 O 97.4 99.3 167.4 80.5 97.1 REMARK 620 N 1 2 3 4 5 DBREF 8D2Y A 1 465 UNP Q8ZNC4 DOKDC_SALTY 1 465 SEQADV 8D2Y PHE A 430 UNP Q8ZNC4 TYR 430 ENGINEERED MUTATION SEQADV 8D2Y LEU A 466 UNP Q8ZNC4 EXPRESSION TAG SEQADV 8D2Y ALA A 467 UNP Q8ZNC4 EXPRESSION TAG SEQADV 8D2Y ALA A 468 UNP Q8ZNC4 EXPRESSION TAG SEQADV 8D2Y ALA A 469 UNP Q8ZNC4 EXPRESSION TAG SEQADV 8D2Y LEU A 470 UNP Q8ZNC4 EXPRESSION TAG SEQADV 8D2Y GLU A 471 UNP Q8ZNC4 EXPRESSION TAG SEQADV 8D2Y HIS A 472 UNP Q8ZNC4 EXPRESSION TAG SEQADV 8D2Y HIS A 473 UNP Q8ZNC4 EXPRESSION TAG SEQADV 8D2Y HIS A 474 UNP Q8ZNC4 EXPRESSION TAG SEQADV 8D2Y HIS A 475 UNP Q8ZNC4 EXPRESSION TAG SEQADV 8D2Y HIS A 476 UNP Q8ZNC4 EXPRESSION TAG SEQADV 8D2Y HIS A 477 UNP Q8ZNC4 EXPRESSION TAG SEQRES 1 A 477 MET THR ASP SER ILE MET GLN ASN TYR ASN GLN LEU ARG SEQRES 2 A 477 GLU GLN VAL ILE ASN GLY ASP ARG ARG PHE GLN HIS LYS SEQRES 3 A 477 ASP GLY HIS LEU CYS PHE GLU GLY VAL ASP LEU ASP ALA SEQRES 4 A 477 LEU ALA ARG GLN TYR PRO THR PRO PHE TYR VAL PHE SER SEQRES 5 A 477 GLU PRO GLU ILE ILE ARG ASN ILE HIS GLU ILE GLN GLN SEQRES 6 A 477 ALA PHE ALA ALA HIS LYS ASN THR LYS THR PHE PHE ALA SEQRES 7 A 477 SER LLP THR CYS SER VAL MET GLY VAL LEU LYS ALA ILE SEQRES 8 A 477 ARG ASP ALA GLY ILE CYS ALA GLU ALA ASN SER GLN TYR SEQRES 9 A 477 GLU VAL ARG LYS CYS LEU GLU ILE GLY PHE ARG GLY ASP SEQRES 10 A 477 GLN ILE VAL PHE ASN GLY VAL VAL LYS LYS PRO ALA ASP SEQRES 11 A 477 LEU GLU TYR ALA ILE ALA ASN ASP LEU TYR LEU ILE ASN SEQRES 12 A 477 VAL ASP SER LEU TYR GLU LEU GLU HIS ILE ASP ALA ILE SEQRES 13 A 477 SER ARG LYS LEU LYS LYS VAL ALA ASN VAL CYS VAL ARG SEQRES 14 A 477 VAL GLU PRO ASN VAL PRO SER ALA THR HIS ALA GLU LEU SEQRES 15 A 477 VAL THR ALA PHE HIS ALA LYS SER GLY LEU ASP LEU GLU SEQRES 16 A 477 GLN ALA GLU GLU THR CYS ARG ARG ILE LEU ALA MET PRO SEQRES 17 A 477 TYR VAL HIS LEU ARG GLY LEU HIS MET HIS VAL GLY ASP SEQRES 18 A 477 GLN VAL PRO GLU SER GLU PRO PHE ALA LYS ALA THR LYS SEQRES 19 A 477 VAL LEU VAL ASP GLU SER ARG ARG LEU GLU GLU VAL LEU SEQRES 20 A 477 GLY ILE LYS PHE ASP LEU ILE ASN VAL GLY GLY GLY ILE SEQRES 21 A 477 PRO VAL PRO TYR LYS TYR ASP ASP GLU ASN GLY ASP PRO SEQRES 22 A 477 LEU LYS ASP ASN MET TYR ALA GLY ILE THR ALA GLN ASP SEQRES 23 A 477 PHE ALA ASP ALA VAL ILE ARG GLU VAL HIS LYS TRP ARG SEQRES 24 A 477 THR ASP VAL GLU ILE CYS ILE GLU PRO GLY ARG LYS VAL SEQRES 25 A 477 THR GLY SER ALA ALA VAL LEU LEU THR GLU VAL SER CYS SEQRES 26 A 477 GLU LYS ARG LYS THR ASN TYR ASP LEU ASN GLY ASN VAL SEQRES 27 A 477 GLU CYS HIS VAL GLU TRP LYS PHE VAL ASP ALA GLY TYR SEQRES 28 A 477 SER VAL LEU SER ASP SER GLN HIS PHE ASP TRP PHE PHE SEQRES 29 A 477 TYR VAL TYR ASN ALA SER ARG MET THR ALA ALA HIS ASP SEQRES 30 A 477 ALA TRP ILE LYS LEU ALA GLY PRO LEU CYS ASP GLY GLY SEQRES 31 A 477 ASP TYR PHE HIS MET GLY VAL LYS GLY GLU GLU PHE LEU SEQRES 32 A 477 LEU PRO LYS GLU THR HIS VAL GLY ASP ILE VAL ALA PHE SEQRES 33 A 477 LEU ASP ALA GLY ALA TYR THR ILE GLU SER GLN THR VAL SEQRES 34 A 477 PHE ASN ASN ARG PRO ARG THR GLY VAL VAL MET ILE ASP SEQRES 35 A 477 LYS ASN GLY ASP THR ARG LEU ILE ARG ARG GLU ASP SER SEQRES 36 A 477 TYR GLU ASP MET VAL LYS TYR ASP ILE TYR LEU ALA ALA SEQRES 37 A 477 ALA LEU GLU HIS HIS HIS HIS HIS HIS MODRES 8D2Y LLP A 80 LYS MODIFIED RESIDUE HET LLP A 80 42 HET DMS A 501 10 HET EDO A 502 10 HET DMS A 503 10 HET EPE A 504 32 HET ACT A 505 7 HET DMS A 506 10 HET ACT A 507 7 HET EDO A 508 10 HET GOL A 509 14 HET GOL A 510 14 HET CL A 511 1 HET K A 512 1 HETNAM LLP (2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5- HETNAM 2 LLP (PHOSPHONOOXYMETHYL)PYRIDIN-4- HETNAM 3 LLP YL]METHYLIDENEAMINO]HEXANOIC ACID HETNAM DMS DIMETHYL SULFOXIDE HETNAM EDO 1,2-ETHANEDIOL HETNAM EPE 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID HETNAM ACT ACETATE ION HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETNAM K POTASSIUM ION HETSYN LLP N'-PYRIDOXYL-LYSINE-5'-MONOPHOSPHATE HETSYN EDO ETHYLENE GLYCOL HETSYN EPE HEPES HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 1 LLP C14 H22 N3 O7 P FORMUL 2 DMS 3(C2 H6 O S) FORMUL 3 EDO 2(C2 H6 O2) FORMUL 5 EPE C8 H18 N2 O4 S FORMUL 6 ACT 2(C2 H3 O2 1-) FORMUL 10 GOL 2(C3 H8 O3) FORMUL 12 CL CL 1- FORMUL 13 K K 1+ FORMUL 14 HOH *656(H2 O) HELIX 1 AA1 MET A 1 ASP A 20 1 20 HELIX 2 AA2 LEU A 37 TYR A 44 1 8 HELIX 3 AA3 GLU A 53 PHE A 67 1 15 HELIX 4 AA4 LLP A 80 CYS A 82 5 3 HELIX 5 AA5 VAL A 84 ALA A 94 1 11 HELIX 6 AA6 SER A 102 GLY A 113 1 12 HELIX 7 AA7 ARG A 115 ASP A 117 5 3 HELIX 8 AA8 LYS A 127 ASN A 137 1 11 HELIX 9 AA9 SER A 146 LYS A 161 1 16 HELIX 10 AB1 THR A 184 ALA A 188 1 5 HELIX 11 AB2 ASP A 193 GLU A 195 5 3 HELIX 12 AB3 GLN A 196 MET A 207 1 12 HELIX 13 AB4 SER A 226 GLY A 248 1 23 HELIX 14 AB5 ASP A 267 GLY A 271 5 5 HELIX 15 AB6 THR A 283 LYS A 297 1 15 HELIX 16 AB7 GLY A 309 GLY A 314 1 6 HELIX 17 AB8 SER A 355 PHE A 360 1 6 HELIX 18 AB9 SER A 370 MET A 372 5 3 HELIX 19 AC1 VAL A 429 ARG A 433 5 5 HELIX 20 AC2 SER A 455 TYR A 462 1 8 SHEET 1 AA1 3 PHE A 23 LYS A 26 0 SHEET 2 AA1 3 HIS A 29 PHE A 32 -1 O CYS A 31 N GLN A 24 SHEET 3 AA1 3 VAL A 35 ASP A 36 -1 O VAL A 35 N PHE A 32 SHEET 1 AA2 6 VAL A 366 ASN A 368 0 SHEET 2 AA2 6 ILE A 413 PHE A 416 -1 O ALA A 415 N TYR A 367 SHEET 3 AA2 6 ALA A 317 TYR A 332 -1 N THR A 321 O VAL A 414 SHEET 4 AA2 6 VAL A 338 VAL A 347 -1 O GLU A 339 N ASN A 331 SHEET 5 AA2 6 ALA A 378 ALA A 383 1 O ALA A 383 N LYS A 345 SHEET 6 AA2 6 PHE A 402 LEU A 404 -1 O PHE A 402 N ILE A 380 SHEET 1 AA3 6 VAL A 366 ASN A 368 0 SHEET 2 AA3 6 ILE A 413 PHE A 416 -1 O ALA A 415 N TYR A 367 SHEET 3 AA3 6 ALA A 317 TYR A 332 -1 N THR A 321 O VAL A 414 SHEET 4 AA3 6 PHE A 48 SER A 52 -1 N PHE A 48 O LEU A 320 SHEET 5 AA3 6 GLY A 437 ILE A 441 1 O VAL A 439 N PHE A 51 SHEET 6 AA3 6 THR A 447 ARG A 451 -1 O ILE A 450 N VAL A 438 SHEET 1 AA4 9 THR A 73 ALA A 78 0 SHEET 2 AA4 9 CYS A 97 ALA A 100 1 O GLU A 99 N PHE A 77 SHEET 3 AA4 9 ILE A 119 PHE A 121 1 O VAL A 120 N ALA A 100 SHEET 4 AA4 9 LEU A 141 VAL A 144 1 O LEU A 141 N PHE A 121 SHEET 5 AA4 9 ALA A 164 ARG A 169 1 O ARG A 169 N VAL A 144 SHEET 6 AA4 9 VAL A 210 HIS A 216 1 O HIS A 211 N ALA A 164 SHEET 7 AA4 9 LEU A 253 ASN A 255 1 O ASN A 255 N LEU A 215 SHEET 8 AA4 9 GLU A 303 ILE A 306 1 O CYS A 305 N ILE A 254 SHEET 9 AA4 9 THR A 73 ALA A 78 1 N PHE A 76 O ILE A 306 LINK C ASER A 79 N LLP A 80 1555 1555 1.32 LINK C BSER A 79 N LLP A 80 1555 1555 1.31 LINK C LLP A 80 N THR A 81 1555 1555 1.32 LINK O ILE A 204 K K A 512 1555 1555 2.84 LINK O LEU A 205 K K A 512 1555 1555 2.92 LINK O MET A 207 K K A 512 1555 1555 2.63 LINK O VAL A 210 K K A 512 1555 1555 2.58 LINK K K A 512 O HOH A 827 1555 1555 2.77 LINK K K A 512 O HOH A1075 1555 1555 3.10 CISPEP 1 THR A 46 PRO A 47 0 -3.24 CRYST1 139.740 50.740 73.320 90.00 120.80 90.00 C 1 2 1 4 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 0.007156 0.000000 0.004266 0.00000 SCALE2 0.000000 0.019708 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015878 0.00000