HEADER LYASE 21-JUN-25 9P7Q TITLE 273K HUMAN S-ADENOSYLMETHIONINE DECARBOXYLASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: S-ADENOSYLMETHIONINE DECARBOXYLASE BETA CHAIN; COMPND 3 CHAIN: B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: S-ADENOSYLMETHIONINE DECARBOXYLASE ALPHA CHAIN; COMPND 7 CHAIN: A; COMPND 8 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: AMD1, AMD; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 GENE: AMD1, AMD; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS POLYAMINE BIOSYNTHESIS, DECARBOXYLASE, ADOMET, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR J.R.PATEL,T.J.BONZON,T.BAHKT,O.O.FAGBOHUN,J.A.CLINGER REVDAT 2 08-OCT-25 9P7Q 1 JRNL REVDAT 1 17-SEP-25 9P7Q 0 JRNL AUTH J.R.PATEL,T.J.BONZON,T.F.BAKHT,O.O.FAGBOHUN,J.A.CLINGER JRNL TITL MULTI-TEMPERATURE CRYSTALLOGRAPHY OF S-ADENOSYLMETHIONINE JRNL TITL 2 DECARBOXYLASE OBSERVES DYNAMIC LOOP MOTIONS. JRNL REF BIOMOLECULES V. 15 2025 JRNL REFN ESSN 2218-273X JRNL PMID 41008581 JRNL DOI 10.3390/BIOM15091274 REMARK 2 REMARK 2 RESOLUTION. 2.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.21.2_5419 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) : 2.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 34.86 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.330 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 14760 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.222 REMARK 3 R VALUE (WORKING SET) : 0.220 REMARK 3 FREE R VALUE : 0.259 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.360 REMARK 3 FREE R VALUE TEST SET COUNT : 791 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 34.8600 - 4.0100 0.98 2439 130 0.1818 0.2182 REMARK 3 2 4.0100 - 3.1800 0.96 2352 119 0.1971 0.2234 REMARK 3 3 3.1800 - 2.7800 0.98 2379 129 0.2489 0.3108 REMARK 3 4 2.7800 - 2.5200 0.99 2354 155 0.2669 0.3157 REMARK 3 5 2.5200 - 2.3400 0.93 2231 128 0.2630 0.2855 REMARK 3 6 2.3400 - 2.2100 0.93 2215 130 0.2784 0.3100 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) : 0.254 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.866 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 11.01 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.41 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 2568 REMARK 3 ANGLE : 1.098 3464 REMARK 3 CHIRALITY : 0.059 373 REMARK 3 PLANARITY : 0.019 442 REMARK 3 DIHEDRAL : 15.742 946 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 8 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN B AND RESID 6:36 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.474 10.136 20.489 REMARK 3 T TENSOR REMARK 3 T11: 0.1436 T22: 0.1289 REMARK 3 T33: 0.1140 T12: 0.0283 REMARK 3 T13: 0.0195 T23: -0.0798 REMARK 3 L TENSOR REMARK 3 L11: 3.8179 L22: 5.5703 REMARK 3 L33: 5.0412 L12: 0.3182 REMARK 3 L13: 1.1797 L23: -0.6372 REMARK 3 S TENSOR REMARK 3 S11: 0.2169 S12: -0.2854 S13: -0.4125 REMARK 3 S21: 0.0833 S22: -0.0618 S23: 0.0657 REMARK 3 S31: 0.0731 S32: -0.1246 S33: -0.1394 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN B AND RESID 37:47 ) REMARK 3 ORIGIN FOR THE GROUP (A): -35.092 19.839 13.953 REMARK 3 T TENSOR REMARK 3 T11: 0.3008 T22: 0.3488 REMARK 3 T33: 0.2873 T12: 0.1308 REMARK 3 T13: 0.1199 T23: 0.1233 REMARK 3 L TENSOR REMARK 3 L11: 8.2320 L22: 2.1939 REMARK 3 L33: 6.8507 L12: -0.7506 REMARK 3 L13: 0.7843 L23: 2.2646 REMARK 3 S TENSOR REMARK 3 S11: 0.2065 S12: 0.4088 S13: 0.5160 REMARK 3 S21: -0.3761 S22: -0.0642 S23: 0.2274 REMARK 3 S31: -0.8364 S32: -0.0734 S33: -0.1776 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN B AND RESID 48:56 ) REMARK 3 ORIGIN FOR THE GROUP (A): -29.784 14.925 8.104 REMARK 3 T TENSOR REMARK 3 T11: 0.2733 T22: 0.4797 REMARK 3 T33: 0.1890 T12: 0.0725 REMARK 3 T13: 0.0411 T23: 0.0244 REMARK 3 L TENSOR REMARK 3 L11: 4.3882 L22: 6.3728 REMARK 3 L33: 9.1713 L12: -1.8131 REMARK 3 L13: -2.0784 L23: 3.9775 REMARK 3 S TENSOR REMARK 3 S11: -0.3673 S12: 0.5910 S13: -0.0581 REMARK 3 S21: -0.3444 S22: 0.9394 S23: -0.1420 REMARK 3 S31: -1.0270 S32: 0.3903 S33: -0.6021 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN B AND RESID 57:67 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.285 8.282 10.590 REMARK 3 T TENSOR REMARK 3 T11: 0.2805 T22: 0.3653 REMARK 3 T33: 0.1687 T12: 0.0292 REMARK 3 T13: -0.0452 T23: -0.0060 REMARK 3 L TENSOR REMARK 3 L11: 4.2503 L22: 5.6671 REMARK 3 L33: 2.0820 L12: 0.1344 REMARK 3 L13: -3.4623 L23: -6.4302 REMARK 3 S TENSOR REMARK 3 S11: 0.0910 S12: 0.2232 S13: -0.1939 REMARK 3 S21: 0.6674 S22: -0.2220 S23: -0.2369 REMARK 3 S31: -0.1120 S32: -0.1596 S33: 0.1888 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: ( CHAIN A AND RESID 69:162 ) REMARK 3 ORIGIN FOR THE GROUP (A): -23.246 15.551 25.972 REMARK 3 T TENSOR REMARK 3 T11: 0.2157 T22: 0.1731 REMARK 3 T33: 0.2099 T12: 0.0204 REMARK 3 T13: 0.0660 T23: -0.0154 REMARK 3 L TENSOR REMARK 3 L11: 4.0128 L22: 1.4111 REMARK 3 L33: 3.2995 L12: 0.1631 REMARK 3 L13: 1.6261 L23: 0.4669 REMARK 3 S TENSOR REMARK 3 S11: 0.0559 S12: -0.1626 S13: 0.4886 REMARK 3 S21: 0.0308 S22: 0.0167 S23: 0.0074 REMARK 3 S31: -0.2733 S32: 0.0641 S33: -0.0742 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: ( CHAIN A AND RESID 163:192 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.613 4.950 19.322 REMARK 3 T TENSOR REMARK 3 T11: 0.1820 T22: 0.1715 REMARK 3 T33: 0.2223 T12: -0.0019 REMARK 3 T13: -0.0524 T23: -0.0401 REMARK 3 L TENSOR REMARK 3 L11: 1.8447 L22: 3.6311 REMARK 3 L33: 3.3308 L12: -0.2017 REMARK 3 L13: 2.3319 L23: 0.0283 REMARK 3 S TENSOR REMARK 3 S11: 0.2293 S12: 0.0173 S13: -0.3077 REMARK 3 S21: 0.4399 S22: -0.2439 S23: 0.0236 REMARK 3 S31: 0.1785 S32: -0.0200 S33: -0.0056 REMARK 3 TLS GROUP : 7 REMARK 3 SELECTION: ( CHAIN A AND RESID 193:287 ) REMARK 3 ORIGIN FOR THE GROUP (A): -15.257 4.557 8.558 REMARK 3 T TENSOR REMARK 3 T11: 0.1672 T22: 0.3018 REMARK 3 T33: 0.1912 T12: 0.0458 REMARK 3 T13: -0.0100 T23: -0.0532 REMARK 3 L TENSOR REMARK 3 L11: 3.8651 L22: 2.0531 REMARK 3 L33: 4.1008 L12: 1.3180 REMARK 3 L13: -0.3137 L23: -0.2705 REMARK 3 S TENSOR REMARK 3 S11: 0.0041 S12: 0.6103 S13: -0.2506 REMARK 3 S21: -0.2962 S22: 0.0693 S23: -0.1161 REMARK 3 S31: 0.2921 S32: 0.2647 S33: -0.0575 REMARK 3 TLS GROUP : 8 REMARK 3 SELECTION: ( CHAIN A AND RESID 288:328 ) REMARK 3 ORIGIN FOR THE GROUP (A): -8.450 0.675 26.151 REMARK 3 T TENSOR REMARK 3 T11: 0.3015 T22: 0.2112 REMARK 3 T33: 0.1651 T12: -0.0056 REMARK 3 T13: -0.0551 T23: 0.0451 REMARK 3 L TENSOR REMARK 3 L11: 5.1394 L22: 4.1587 REMARK 3 L33: 5.8490 L12: -1.5808 REMARK 3 L13: -0.4925 L23: 0.0297 REMARK 3 S TENSOR REMARK 3 S11: -0.0525 S12: -0.2927 S13: -0.1837 REMARK 3 S21: 0.2664 S22: 0.0443 S23: -0.0641 REMARK 3 S31: 0.6511 S32: 0.2238 S33: 0.0583 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 9P7Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 23-JUN-25. REMARK 100 THE DEPOSITION ID IS D_1000297039. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAY-25 REMARK 200 TEMPERATURE (KELVIN) : 273 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97946 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : STARANISO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14760 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.210 REMARK 200 RESOLUTION RANGE LOW (A) : 34.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 97.4 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.28600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 4.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.27 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.20 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 35.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.02 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 4MG/ML ENZYME IN 200MM NACL 50MM HEPES REMARK 280 PH 7.5 1:1 TO RESERVOIR SOLUTION CONTAINING 4-8% PEG 8000 AND REMARK 280 50MM TRIS-HCL PH 8.5, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 295K 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 48.48900 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.50900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 48.48900 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.50900 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: 7210 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 13420 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -38.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 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 CL CL A 403 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 586 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 B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 HIS B -9 REMARK 465 HIS B -8 REMARK 465 HIS B -7 REMARK 465 HIS B -6 REMARK 465 GLU B -5 REMARK 465 ASN B -4 REMARK 465 LEU B -3 REMARK 465 TYR B -2 REMARK 465 PHE B -1 REMARK 465 GLN B 0 REMARK 465 GLY B 1 REMARK 465 GLU B 2 REMARK 465 ALA B 3 REMARK 465 ALA B 4 REMARK 465 HIS B 5 REMARK 465 GLN B 22 REMARK 465 PRO B 23 REMARK 465 ASP B 24 REMARK 465 ALA B 25 REMARK 465 ASN B 26 REMARK 465 LYS A 291 REMARK 465 CYS A 292 REMARK 465 ARG A 293 REMARK 465 THR A 294 REMARK 465 VAL A 295 REMARK 465 LEU A 296 REMARK 465 ALA A 297 REMARK 465 SER A 298 REMARK 465 PRO A 299 REMARK 465 GLN A 329 REMARK 465 GLN A 330 REMARK 465 GLN A 331 REMARK 465 GLN A 332 REMARK 465 GLN A 333 REMARK 465 SER A 334 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 GLN B 27 CG CD OE1 NE2 REMARK 470 ARG A 168 CG CD NE CZ NH1 NH2 REMARK 470 ILE A 170 CG1 CG2 CD1 REMARK 470 GLN A 172 CG CD OE1 NE2 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 HG SER A 229 O HOH A 504 1.57 REMARK 500 HD22 ASN A 138 O HOH A 503 1.58 REMARK 500 OE1 GLU B 61 O HOH B 101 1.89 REMARK 500 OE1 GLN A 123 O HOH A 501 2.07 REMARK 500 O PRO A 186 O HOH A 502 2.11 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 B 109 O HOH A 573 3455 1.86 REMARK 500 SD MET A 314 O HOH A 559 2556 1.94 REMARK 500 O HOH B 123 O HOH A 587 4445 2.08 REMARK 500 CG MET A 314 O HOH A 559 2556 2.19 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 PYR A 68 C SER A 69 N 0.167 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 PYR A 68 O - C - N ANGL. DEV. = 10.5 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 B 48 42.30 75.90 REMARK 500 SER A 73 -162.00 -117.67 REMARK 500 CYS A 82 -158.87 -134.33 REMARK 500 PRO A 126 42.76 -104.30 REMARK 500 SER A 154 -128.69 -150.95 REMARK 500 SER A 154 -129.90 -150.95 REMARK 500 CYS A 156 -169.54 -113.54 REMARK 500 CYS A 156 -169.54 -113.27 REMARK 500 GLN A 172 99.74 49.18 REMARK 500 VAL A 198 109.93 -59.47 REMARK 500 PHE A 250 42.38 -154.08 REMARK 500 ASN A 316 -115.73 57.99 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 B 20 0.17 SIDE CHAIN REMARK 500 ARG A 151 0.13 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 VAL B 64 -11.41 REMARK 500 ASP A 155 14.13 REMARK 500 ASP A 155 12.62 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 582 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH A 583 DISTANCE = 6.24 ANGSTROMS REMARK 525 HOH A 584 DISTANCE = 6.86 ANGSTROMS REMARK 525 HOH A 585 DISTANCE = 6.92 ANGSTROMS REMARK 525 HOH A 586 DISTANCE = 6.96 ANGSTROMS REMARK 525 HOH A 587 DISTANCE = 8.11 ANGSTROMS REMARK 525 HOH A 588 DISTANCE = 9.04 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 9P1H RELATED DB: PDB REMARK 900 DATA COLLECTED AT 100K REMARK 900 RELATED ID: 9PBB RELATED DB: PDB REMARK 900 DATA COLLECTED AT 293K DBREF 9P7Q B 2 67 UNP P17707 DCAM_HUMAN 2 67 DBREF 9P7Q A 68 334 UNP P17707 DCAM_HUMAN 68 334 SEQADV 9P7Q MET B -12 UNP P17707 INITIATING METHIONINE SEQADV 9P7Q HIS B -11 UNP P17707 EXPRESSION TAG SEQADV 9P7Q HIS B -10 UNP P17707 EXPRESSION TAG SEQADV 9P7Q HIS B -9 UNP P17707 EXPRESSION TAG SEQADV 9P7Q HIS B -8 UNP P17707 EXPRESSION TAG SEQADV 9P7Q HIS B -7 UNP P17707 EXPRESSION TAG SEQADV 9P7Q HIS B -6 UNP P17707 EXPRESSION TAG SEQADV 9P7Q GLU B -5 UNP P17707 EXPRESSION TAG SEQADV 9P7Q ASN B -4 UNP P17707 EXPRESSION TAG SEQADV 9P7Q LEU B -3 UNP P17707 EXPRESSION TAG SEQADV 9P7Q TYR B -2 UNP P17707 EXPRESSION TAG SEQADV 9P7Q PHE B -1 UNP P17707 EXPRESSION TAG SEQADV 9P7Q GLN B 0 UNP P17707 EXPRESSION TAG SEQADV 9P7Q GLY B 1 UNP P17707 EXPRESSION TAG SEQADV 9P7Q PYR A 68 UNP P17707 SER 68 MODIFIED RESIDUE SEQRES 1 B 80 MET HIS HIS HIS HIS HIS HIS GLU ASN LEU TYR PHE GLN SEQRES 2 B 80 GLY GLU ALA ALA HIS PHE PHE GLU GLY THR GLU LYS LEU SEQRES 3 B 80 LEU GLU VAL TRP PHE SER ARG GLN GLN PRO ASP ALA ASN SEQRES 4 B 80 GLN GLY SER GLY ASP LEU ARG THR ILE PRO ARG SER GLU SEQRES 5 B 80 TRP ASP ILE LEU LEU LYS ASP VAL GLN CYS SER ILE ILE SEQRES 6 B 80 SER VAL THR LYS THR ASP LYS GLN GLU ALA TYR VAL LEU SEQRES 7 B 80 SER GLU SEQRES 1 A 267 PYR SER MET PHE VAL SER LYS ARG ARG PHE ILE LEU LYS SEQRES 2 A 267 THR CYS GLY THR THR LEU LEU LEU LYS ALA LEU VAL PRO SEQRES 3 A 267 LEU LEU LYS LEU ALA ARG ASP TYR SER GLY PHE ASP SER SEQRES 4 A 267 ILE GLN SER PHE PHE TYR SER ARG LYS ASN PHE MET LYS SEQRES 5 A 267 PRO SER HIS GLN GLY TYR PRO HIS ARG ASN PHE GLN GLU SEQRES 6 A 267 GLU ILE GLU PHE LEU ASN ALA ILE PHE PRO ASN GLY ALA SEQRES 7 A 267 ALA TYR CYS MET GLY ARG MET ASN SER ASP CYS TRP TYR SEQRES 8 A 267 LEU TYR THR LEU ASP PHE PRO GLU SER ARG VAL ILE SER SEQRES 9 A 267 GLN PRO ASP GLN THR LEU GLU ILE LEU MET SER GLU LEU SEQRES 10 A 267 ASP PRO ALA VAL MET ASP GLN PHE TYR MET LYS ASP GLY SEQRES 11 A 267 VAL THR ALA LYS ASP VAL THR ARG GLU SER GLY ILE ARG SEQRES 12 A 267 ASP LEU ILE PRO GLY SER VAL ILE ASP ALA THR MET PHE SEQRES 13 A 267 ASN PRO CYS GLY TYR SER MET ASN GLY MET LYS SER ASP SEQRES 14 A 267 GLY THR TYR TRP THR ILE HIS ILE THR PRO GLU PRO GLU SEQRES 15 A 267 PHE SER TYR VAL SER PHE GLU THR ASN LEU SER GLN THR SEQRES 16 A 267 SER TYR ASP ASP LEU ILE ARG LYS VAL VAL GLU VAL PHE SEQRES 17 A 267 LYS PRO GLY LYS PHE VAL THR THR LEU PHE VAL ASN GLN SEQRES 18 A 267 SER SER LYS CYS ARG THR VAL LEU ALA SER PRO GLN LYS SEQRES 19 A 267 ILE GLU GLY PHE LYS ARG LEU ASP CYS GLN SER ALA MET SEQRES 20 A 267 PHE ASN ASP TYR ASN PHE VAL PHE THR SER PHE ALA LYS SEQRES 21 A 267 LYS GLN GLN GLN GLN GLN SER HET PYR A 68 8 HET TRS A 401 20 HET PUT A 402 18 HET CL A 403 1 HETNAM PYR PYRUVIC ACID HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETNAM PUT 1,4-DIAMINOBUTANE HETNAM CL CHLORIDE ION HETSYN TRS TRIS BUFFER HETSYN PUT PUTRESCINE FORMUL 2 PYR C3 H4 O3 FORMUL 3 TRS C4 H12 N O3 1+ FORMUL 4 PUT C4 H12 N2 FORMUL 5 CL CL 1- FORMUL 6 HOH *111(H2 O) HELIX 1 AA1 ASP B 31 ILE B 35 5 5 HELIX 2 AA2 PRO B 36 GLN B 48 1 13 HELIX 3 AA3 LEU A 86 LYS A 89 5 4 HELIX 4 AA4 ALA A 90 GLY A 103 1 14 HELIX 5 AA5 LYS A 119 GLN A 123 5 5 HELIX 6 AA6 ASN A 129 PHE A 141 1 13 HELIX 7 AA7 ASP A 185 GLN A 191 1 7 HELIX 8 AA8 THR A 199 SER A 207 1 9 HELIX 9 AA9 ILE A 209 ILE A 213 5 5 HELIX 10 AB1 GLU A 247 PHE A 250 5 4 HELIX 11 AB2 TYR A 264 LYS A 276 1 13 SHEET 1 AA1 8 SER B 50 LYS B 56 0 SHEET 2 AA1 8 GLU B 61 SER B 66 -1 O VAL B 64 N ILE B 52 SHEET 3 AA1 8 SER A 69 VAL A 72 -1 O MET A 70 N TYR B 63 SHEET 4 AA1 8 ARG A 76 THR A 81 -1 O LYS A 80 N SER A 69 SHEET 5 AA1 8 LYS B 12 PHE B 18 -1 N LYS B 12 O THR A 81 SHEET 6 AA1 8 ILE A 107 LYS A 115 -1 O GLN A 108 N TRP B 17 SHEET 7 AA1 8 CYS A 156 LEU A 162 -1 O TYR A 160 N TYR A 112 SHEET 8 AA1 8 GLY A 144 GLY A 150 -1 N ALA A 145 O THR A 161 SHEET 1 AA2 8 VAL A 217 MET A 222 0 SHEET 2 AA2 8 TYR A 228 MET A 233 -1 O MET A 233 N VAL A 217 SHEET 3 AA2 8 TYR A 239 THR A 245 -1 O ILE A 244 N TYR A 228 SHEET 4 AA2 8 TYR A 252 THR A 257 -1 O TYR A 252 N THR A 245 SHEET 5 AA2 8 GLN A 175 SER A 182 -1 N MET A 181 O VAL A 253 SHEET 6 AA2 8 LYS A 279 ASN A 287 -1 O LYS A 279 N SER A 182 SHEET 7 AA2 8 TYR A 318 LYS A 327 -1 O PHE A 325 N PHE A 280 SHEET 8 AA2 8 PHE A 305 PHE A 315 -1 N PHE A 315 O TYR A 318 LINK C PYR A 68 N SER A 69 1555 1555 1.50 CISPEP 1 TYR A 125 PRO A 126 0 3.23 CISPEP 2 ASN A 224 PRO A 225 0 -1.15 CRYST1 96.978 45.018 72.061 90.00 105.11 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 0.010312 0.000000 0.002784 0.00000 SCALE2 0.000000 0.022213 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014374 0.00000 CONECT 928 929 930 936 CONECT 929 928 CONECT 930 928 931 932 CONECT 931 930 CONECT 932 930 933 934 935 CONECT 933 932 CONECT 934 932 CONECT 935 932 CONECT 936 928 CONECT 4922 4923 4924 4925 4926 CONECT 4923 4922 4927 4930 4931 CONECT 4924 4922 4928 4932 4933 CONECT 4925 4922 4929 4934 4935 CONECT 4926 4922 4936 4937 4938 CONECT 4927 4923 4939 CONECT 4928 4924 4940 CONECT 4929 4925 4941 CONECT 4930 4923 CONECT 4931 4923 CONECT 4932 4924 CONECT 4933 4924 CONECT 4934 4925 CONECT 4935 4925 CONECT 4936 4926 CONECT 4937 4926 CONECT 4938 4926 CONECT 4939 4927 CONECT 4940 4928 CONECT 4941 4929 CONECT 4942 4943 4948 4949 CONECT 4943 4942 4944 4950 4951 CONECT 4944 4943 4945 4952 4953 CONECT 4945 4944 4946 4954 4955 CONECT 4946 4945 4947 4956 4957 CONECT 4947 4946 4958 4959 CONECT 4948 4942 CONECT 4949 4942 CONECT 4950 4943 CONECT 4951 4943 CONECT 4952 4944 CONECT 4953 4944 CONECT 4954 4945 CONECT 4955 4945 CONECT 4956 4946 CONECT 4957 4946 CONECT 4958 4947 CONECT 4959 4947 MASTER 544 0 4 11 16 0 0 6 2612 2 47 28 END