HEADER TRANSFERASE 09-MAR-18 6FXM TITLE CRYSTAL STRUCTURE OF FULL-LENGTH HUMAN LYSYL HYDROXYLASE LH3 - TITLE 2 COCRYSTAL WITH MN2+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROCOLLAGEN-LYSINE,2-OXOGLUTARATE 5-DIOXYGENASE 3; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LYSYL HYDROXYLASE 3,LH3; COMPND 5 EC: 1.14.11.4; 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: PLOD3; SOURCE 6 EXPRESSION_SYSTEM: HOMO SAPIENS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 8 EXPRESSION_SYSTEM_CELL: HELA; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PPURO-DHFR KEYWDS LYSYL HYDROXYLASE, GALACOSYLTRANSFERASE, GLUCOSYLTRANSFERASE, KEYWDS 2 COLLAGEN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR L.SCIETTI,A.CHIAPPARINO,F.DE GIORGI,M.FUMAGALLI,L.KHORIAULI, AUTHOR 2 S.NERGADZE,S.BASU,V.OLIERIC,B.BANUSHI,E.GIULOTTO,P.GISSEN,F.FORNERIS REVDAT 2 29-JUL-20 6FXM 1 COMPND REMARK HETNAM LINK REVDAT 2 2 1 SITE ATOM REVDAT 1 22-AUG-18 6FXM 0 JRNL AUTH L.SCIETTI,A.CHIAPPARINO,F.DE GIORGI,M.FUMAGALLI,L.KHORIAULI, JRNL AUTH 2 S.NERGADZE,S.BASU,V.OLIERIC,L.CUCCA,B.BANUSHI,A.PROFUMO, JRNL AUTH 3 E.GIULOTTO,P.GISSEN,F.FORNERIS JRNL TITL MOLECULAR ARCHITECTURE OF THE MULTIFUNCTIONAL COLLAGEN LYSYL JRNL TITL 2 HYDROXYLASE AND GLYCOSYLTRANSFERASE LH3. JRNL REF NAT COMMUN V. 9 3163 2018 JRNL REFN ESSN 2041-1723 JRNL PMID 30089812 JRNL DOI 10.1038/S41467-018-05631-5 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.37 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 63945 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.230 REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3132 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 37.3758 - 5.8771 1.00 2946 144 0.1788 0.1659 REMARK 3 2 5.8771 - 4.6677 1.00 2835 158 0.1601 0.1925 REMARK 3 3 4.6677 - 4.0785 1.00 2806 149 0.1445 0.1689 REMARK 3 4 4.0785 - 3.7059 0.99 2756 155 0.1691 0.1927 REMARK 3 5 3.7059 - 3.4405 1.00 2798 141 0.1908 0.2175 REMARK 3 6 3.4405 - 3.2378 0.99 2772 127 0.2047 0.2386 REMARK 3 7 3.2378 - 3.0757 1.00 2783 129 0.2174 0.2393 REMARK 3 8 3.0757 - 2.9419 1.00 2766 144 0.2276 0.2596 REMARK 3 9 2.9419 - 2.8287 1.00 2753 151 0.2382 0.2601 REMARK 3 10 2.8287 - 2.7311 1.00 2741 162 0.2658 0.3166 REMARK 3 11 2.7311 - 2.6457 1.00 2763 131 0.2819 0.3429 REMARK 3 12 2.6457 - 2.5701 0.99 2690 165 0.2874 0.3104 REMARK 3 13 2.5701 - 2.5025 0.99 2752 131 0.3324 0.3883 REMARK 3 14 2.5025 - 2.4414 0.99 2756 144 0.3418 0.3657 REMARK 3 15 2.4414 - 2.3859 0.99 2735 142 0.3454 0.3719 REMARK 3 16 2.3859 - 2.3352 1.00 2735 137 0.3692 0.3826 REMARK 3 17 2.3352 - 2.2884 1.00 2765 135 0.4038 0.4425 REMARK 3 18 2.2884 - 2.2453 0.99 2706 133 0.4358 0.4553 REMARK 3 19 2.2453 - 2.2052 1.00 2769 139 0.4700 0.4892 REMARK 3 20 2.2052 - 2.1678 1.00 2731 126 0.4753 0.5446 REMARK 3 21 2.1678 - 2.1328 0.99 2737 140 0.5104 0.6162 REMARK 3 22 2.1328 - 2.1000 0.99 2718 149 0.5410 0.5281 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.310 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 39.860 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 : 0.003 5811 REMARK 3 ANGLE : 0.618 7894 REMARK 3 CHIRALITY : 0.044 830 REMARK 3 PLANARITY : 0.004 1025 REMARK 3 DIHEDRAL : 15.475 3433 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 5 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 33 THROUGH 100 ) REMARK 3 ORIGIN FOR THE GROUP (A): 70.5587 30.7908 146.8295 REMARK 3 T TENSOR REMARK 3 T11: 0.5383 T22: 0.3415 REMARK 3 T33: 0.3159 T12: 0.0314 REMARK 3 T13: -0.0260 T23: 0.0017 REMARK 3 L TENSOR REMARK 3 L11: 0.0167 L22: 0.0130 REMARK 3 L33: 0.0192 L12: 0.0082 REMARK 3 L13: 0.0015 L23: 0.0188 REMARK 3 S TENSOR REMARK 3 S11: -0.2213 S12: 0.1583 S13: -0.0622 REMARK 3 S21: -0.1557 S22: 0.0246 S23: -0.2277 REMARK 3 S31: -0.3545 S32: 0.0866 S33: -0.0003 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 101 THROUGH 242 ) REMARK 3 ORIGIN FOR THE GROUP (A): 57.4698 22.9206 145.7471 REMARK 3 T TENSOR REMARK 3 T11: 0.1163 T22: 0.4624 REMARK 3 T33: 0.1319 T12: 0.2032 REMARK 3 T13: -0.0930 T23: -0.0808 REMARK 3 L TENSOR REMARK 3 L11: 0.4590 L22: 0.8157 REMARK 3 L33: 0.2245 L12: 0.3287 REMARK 3 L13: -0.0157 L23: -0.0512 REMARK 3 S TENSOR REMARK 3 S11: -0.1029 S12: 0.1258 S13: -0.2814 REMARK 3 S21: -0.3364 S22: -0.0153 S23: -0.4079 REMARK 3 S31: -0.2822 S32: -0.4963 S33: -0.1073 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 243 THROUGH 310 ) REMARK 3 ORIGIN FOR THE GROUP (A): 71.4891 25.8466 170.1193 REMARK 3 T TENSOR REMARK 3 T11: 0.1724 T22: 0.2722 REMARK 3 T33: 0.2829 T12: 0.0315 REMARK 3 T13: -0.0490 T23: -0.0384 REMARK 3 L TENSOR REMARK 3 L11: 0.0042 L22: 0.1041 REMARK 3 L33: 0.0854 L12: 0.0367 REMARK 3 L13: -0.0269 L23: -0.0422 REMARK 3 S TENSOR REMARK 3 S11: 0.0632 S12: 0.0737 S13: -0.0906 REMARK 3 S21: 0.1330 S22: -0.0105 S23: -0.1121 REMARK 3 S31: -0.0483 S32: 0.0008 S33: 0.0247 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 311 THROUGH 515 ) REMARK 3 ORIGIN FOR THE GROUP (A): 72.0505 35.7841 183.0134 REMARK 3 T TENSOR REMARK 3 T11: 0.2534 T22: 0.1987 REMARK 3 T33: 0.3047 T12: -0.0243 REMARK 3 T13: -0.0280 T23: 0.0115 REMARK 3 L TENSOR REMARK 3 L11: 0.2906 L22: 0.1350 REMARK 3 L33: 0.1577 L12: 0.1169 REMARK 3 L13: 0.0201 L23: -0.0938 REMARK 3 S TENSOR REMARK 3 S11: 0.0652 S12: -0.0062 S13: 0.0310 REMARK 3 S21: 0.2702 S22: -0.0372 S23: -0.0071 REMARK 3 S31: -0.0287 S32: 0.0153 S33: 0.0003 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 516 THROUGH 738 ) REMARK 3 ORIGIN FOR THE GROUP (A): 77.9689 18.3114 219.2569 REMARK 3 T TENSOR REMARK 3 T11: 0.6290 T22: 0.3696 REMARK 3 T33: 0.2635 T12: -0.0956 REMARK 3 T13: -0.0487 T23: 0.0425 REMARK 3 L TENSOR REMARK 3 L11: 0.1203 L22: 0.1239 REMARK 3 L33: 0.1338 L12: -0.0142 REMARK 3 L13: -0.0059 L23: -0.0423 REMARK 3 S TENSOR REMARK 3 S11: -0.0307 S12: 0.0170 S13: 0.0196 REMARK 3 S21: 0.1760 S22: -0.0207 S23: 0.0199 REMARK 3 S31: -0.0388 S32: 0.0827 S33: -0.0005 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 6FXM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-MAR-18. REMARK 100 THE DEPOSITION ID IS D_1200009098. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-APR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : MASSIF-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9677 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64193 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 REMARK 200 RESOLUTION RANGE LOW (A) : 48.790 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.800 REMARK 200 R MERGE (I) : 0.09500 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.15 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 8.00 REMARK 200 R MERGE FOR SHELL (I) : 2.44400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 0.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SHARP REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 600 MM SODIUM FORMATE, 12% PGA-LM, 100 REMARK 280 MM HEPES/NAOH, 0.5 MM MNCL2, PH 7.8, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 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 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 112.56900 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 112.56900 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 48.63500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.97450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 48.63500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.97450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 112.56900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 48.63500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.97450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 112.56900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 48.63500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.97450 REMARK 290 SMTRY3 8 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 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 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 450.27600 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 985 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1094 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 24 REMARK 465 SER A 25 REMARK 465 ASP A 26 REMARK 465 ARG A 27 REMARK 465 PRO A 28 REMARK 465 ARG A 29 REMARK 465 GLY A 30 REMARK 465 ARG A 31 REMARK 465 ASP A 32 REMARK 465 GLU A 73 REMARK 465 GLU A 74 REMARK 465 TRP A 75 REMARK 465 ARG A 76 REMARK 465 GLY A 77 REMARK 465 GLY A 78 REMARK 465 ASP A 79 REMARK 465 VAL A 80 REMARK 465 ALA A 81 REMARK 465 ARG A 82 REMARK 465 THR A 83 REMARK 465 VAL A 84 REMARK 465 GLY A 85 REMARK 465 THR A 288 REMARK 465 LEU A 289 REMARK 465 PRO A 290 REMARK 465 GLY A 291 REMARK 465 GLY A 292 REMARK 465 GLY A 592 REMARK 465 GLY A 593 REMARK 465 ARG A 594 REMARK 465 HIS A 595 REMARK 465 GLU A 596 REMARK 465 GLY A 603 REMARK 465 TYR A 604 REMARK 465 GLU A 605 REMARK 465 ASN A 606 REMARK 465 ALA A 739 REMARK 465 ALA A 740 REMARK 465 ALA A 741 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 HOH A 975 O HOH A 1101 1.81 REMARK 500 O ASP A 345 O HOH A 901 1.81 REMARK 500 OE2 GLU A 48 O HOH A 902 1.89 REMARK 500 O HOH A 1149 O HOH A 1154 1.91 REMARK 500 O ASP A 611 O HOH A 903 1.93 REMARK 500 O LEU A 638 O HOH A 904 1.96 REMARK 500 NE2 GLN A 543 O HOH A 905 1.96 REMARK 500 O HOH A 1140 O HOH A 1161 1.97 REMARK 500 O HOH A 1011 O HOH A 1026 1.99 REMARK 500 N ASN A 651 O HOH A 906 2.02 REMARK 500 O HOH A 940 O HOH A 941 2.06 REMARK 500 OE1 GLU A 50 O HOH A 907 2.08 REMARK 500 OD2 ASP A 578 O HOH A 908 2.09 REMARK 500 O1 GOL A 804 O HOH A 909 2.10 REMARK 500 O HOH A 1098 O HOH A 1152 2.11 REMARK 500 O HIS A 510 O HOH A 910 2.12 REMARK 500 O HOH A 983 O HOH A 1147 2.12 REMARK 500 NH2 ARG A 628 O HOH A 911 2.12 REMARK 500 OD1 ASP A 190 N LEU A 193 2.12 REMARK 500 OD2 ASP A 102 O HOH A 912 2.12 REMARK 500 N VAL A 610 O HOH A 913 2.13 REMARK 500 O TYR A 730 O HOH A 914 2.15 REMARK 500 OD1 ASP A 102 O HOH A 915 2.15 REMARK 500 OE1 GLU A 386 O HOH A 916 2.15 REMARK 500 OG SER A 142 O HOH A 917 2.16 REMARK 500 OD2 ASP A 189 O HOH A 918 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 TYR A 185 -153.79 -88.46 REMARK 500 PRO A 257 44.71 -88.56 REMARK 500 TYR A 268 -52.07 -120.88 REMARK 500 GLN A 463 -26.54 72.04 REMARK 500 SER A 483 -168.79 -104.77 REMARK 500 SER A 519 -72.47 -41.57 REMARK 500 ARG A 520 51.64 -115.29 REMARK 500 LEU A 571 -52.02 -127.18 REMARK 500 GLU A 660 -106.31 -105.84 REMARK 500 LYS A 705 -70.31 -44.33 REMARK 500 LEU A 715 -48.61 72.72 REMARK 500 HIS A 717 56.55 -108.19 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 MN A 807 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 112 OD2 REMARK 620 2 ASP A 115 OD1 115.0 REMARK 620 3 ASP A 115 OD2 171.6 56.6 REMARK 620 4 HIS A 253 NE2 89.0 94.1 91.2 REMARK 620 5 HOH A1032 O 92.4 72.8 85.4 166.0 REMARK 620 6 HOH A1137 O 100.3 144.5 88.1 90.3 103.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 808 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 597 OD2 REMARK 620 2 ASP A 611 OD1 152.4 REMARK 620 3 ASP A 611 OD2 96.1 58.1 REMARK 620 4 HOH A1007 O 120.2 74.0 91.7 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 A 806 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 667 NE2 REMARK 620 2 ASP A 669 OD1 95.7 REMARK 620 3 HIS A 719 NE2 97.4 119.7 REMARK 620 4 AKG A 805 O2 89.9 95.3 143.1 REMARK 620 5 AKG A 805 O5 99.7 161.6 68.2 74.9 REMARK 620 N 1 2 3 4 DBREF 6FXM A 25 738 UNP O60568 PLOD3_HUMAN 25 738 SEQADV 6FXM SER A 24 UNP O60568 EXPRESSION TAG SEQADV 6FXM ALA A 739 UNP O60568 EXPRESSION TAG SEQADV 6FXM ALA A 740 UNP O60568 EXPRESSION TAG SEQADV 6FXM ALA A 741 UNP O60568 EXPRESSION TAG SEQRES 1 A 718 SER SER ASP ARG PRO ARG GLY ARG ASP PRO VAL ASN PRO SEQRES 2 A 718 GLU LYS LEU LEU VAL ILE THR VAL ALA THR ALA GLU THR SEQRES 3 A 718 GLU GLY TYR LEU ARG PHE LEU ARG SER ALA GLU PHE PHE SEQRES 4 A 718 ASN TYR THR VAL ARG THR LEU GLY LEU GLY GLU GLU TRP SEQRES 5 A 718 ARG GLY GLY ASP VAL ALA ARG THR VAL GLY GLY GLY GLN SEQRES 6 A 718 LYS VAL ARG TRP LEU LYS LYS GLU MET GLU LYS TYR ALA SEQRES 7 A 718 ASP ARG GLU ASP MET ILE ILE MET PHE VAL ASP SER TYR SEQRES 8 A 718 ASP VAL ILE LEU ALA GLY SER PRO THR GLU LEU LEU LYS SEQRES 9 A 718 LYS PHE VAL GLN SER GLY SER ARG LEU LEU PHE SER ALA SEQRES 10 A 718 GLU SER PHE CYS TRP PRO GLU TRP GLY LEU ALA GLU GLN SEQRES 11 A 718 TYR PRO GLU VAL GLY THR GLY LYS ARG PHE LEU ASN SER SEQRES 12 A 718 GLY GLY PHE ILE GLY PHE ALA THR THR ILE HIS GLN ILE SEQRES 13 A 718 VAL ARG GLN TRP LYS TYR LYS ASP ASP ASP ASP ASP GLN SEQRES 14 A 718 LEU PHE TYR THR ARG LEU TYR LEU ASP PRO GLY LEU ARG SEQRES 15 A 718 GLU LYS LEU SER LEU ASN LEU ASP HIS LYS SER ARG ILE SEQRES 16 A 718 PHE GLN ASN LEU ASN GLY ALA LEU ASP GLU VAL VAL LEU SEQRES 17 A 718 LYS PHE ASP ARG ASN ARG VAL ARG ILE ARG ASN VAL ALA SEQRES 18 A 718 TYR ASP THR LEU PRO ILE VAL VAL HIS GLY ASN GLY PRO SEQRES 19 A 718 THR LYS LEU GLN LEU ASN TYR LEU GLY ASN TYR VAL PRO SEQRES 20 A 718 ASN GLY TRP THR PRO GLU GLY GLY CYS GLY PHE CYS ASN SEQRES 21 A 718 GLN ASP ARG ARG THR LEU PRO GLY GLY GLN PRO PRO PRO SEQRES 22 A 718 ARG VAL PHE LEU ALA VAL PHE VAL GLU GLN PRO THR PRO SEQRES 23 A 718 PHE LEU PRO ARG PHE LEU GLN ARG LEU LEU LEU LEU ASP SEQRES 24 A 718 TYR PRO PRO ASP ARG VAL THR LEU PHE LEU HIS ASN ASN SEQRES 25 A 718 GLU VAL PHE HIS GLU PRO HIS ILE ALA ASP SER TRP PRO SEQRES 26 A 718 GLN LEU GLN ASP HIS PHE SER ALA VAL LYS LEU VAL GLY SEQRES 27 A 718 PRO GLU GLU ALA LEU SER PRO GLY GLU ALA ARG ASP MET SEQRES 28 A 718 ALA MET ASP LEU CYS ARG GLN ASP PRO GLU CYS GLU PHE SEQRES 29 A 718 TYR PHE SER LEU ASP ALA ASP ALA VAL LEU THR ASN LEU SEQRES 30 A 718 GLN THR LEU ARG ILE LEU ILE GLU GLU ASN ARG LYS VAL SEQRES 31 A 718 ILE ALA PRO MET LEU SER ARG HIS GLY LYS LEU TRP SER SEQRES 32 A 718 ASN PHE TRP GLY ALA LEU SER PRO ASP GLU TYR TYR ALA SEQRES 33 A 718 ARG SER GLU ASP TYR VAL GLU LEU VAL GLN ARG LYS ARG SEQRES 34 A 718 VAL GLY VAL TRP ASN VAL PRO TYR ILE SER GLN ALA TYR SEQRES 35 A 718 VAL ILE ARG GLY ASP THR LEU ARG MET GLU LEU PRO GLN SEQRES 36 A 718 ARG ASP VAL PHE SER GLY SER ASP THR ASP PRO ASP MET SEQRES 37 A 718 ALA PHE CYS LYS SER PHE ARG ASP LYS GLY ILE PHE LEU SEQRES 38 A 718 HIS LEU SER ASN GLN HIS GLU PHE GLY ARG LEU LEU ALA SEQRES 39 A 718 THR SER ARG TYR ASP THR GLU HIS LEU HIS PRO ASP LEU SEQRES 40 A 718 TRP GLN ILE PHE ASP ASN PRO VAL ASP TRP LYS GLU GLN SEQRES 41 A 718 TYR ILE HIS GLU ASN TYR SER ARG ALA LEU GLU GLY GLU SEQRES 42 A 718 GLY ILE VAL GLU GLN PRO CYS PRO ASP VAL TYR TRP PHE SEQRES 43 A 718 PRO LEU LEU SER GLU GLN MET CYS ASP GLU LEU VAL ALA SEQRES 44 A 718 GLU MET GLU HIS TYR GLY GLN TRP SER GLY GLY ARG HIS SEQRES 45 A 718 GLU ASP SER ARG LEU ALA GLY GLY TYR GLU ASN VAL PRO SEQRES 46 A 718 THR VAL ASP ILE HIS MET LYS GLN VAL GLY TYR GLU ASP SEQRES 47 A 718 GLN TRP LEU GLN LEU LEU ARG THR TYR VAL GLY PRO MET SEQRES 48 A 718 THR GLU SER LEU PHE PRO GLY TYR HIS THR LYS ALA ARG SEQRES 49 A 718 ALA VAL MET ASN PHE VAL VAL ARG TYR ARG PRO ASP GLU SEQRES 50 A 718 GLN PRO SER LEU ARG PRO HIS HIS ASP SER SER THR PHE SEQRES 51 A 718 THR LEU ASN VAL ALA LEU ASN HIS LYS GLY LEU ASP TYR SEQRES 52 A 718 GLU GLY GLY GLY CYS ARG PHE LEU ARG TYR ASP CYS VAL SEQRES 53 A 718 ILE SER SER PRO ARG LYS GLY TRP ALA LEU LEU HIS PRO SEQRES 54 A 718 GLY ARG LEU THR HIS TYR HIS GLU GLY LEU PRO THR THR SEQRES 55 A 718 TRP GLY THR ARG TYR ILE MET VAL SER PHE VAL ASP PRO SEQRES 56 A 718 ALA ALA ALA HET NAG B 1 14 HET NAG B 2 14 HET GOL A 801 6 HET GOL A 802 6 HET GOL A 803 6 HET GOL A 804 6 HET AKG A 805 10 HET FE2 A 806 1 HET MN A 807 1 HET MN A 808 1 HET NAG A 809 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM GOL GLYCEROL HETNAM AKG 2-OXOGLUTARIC ACID HETNAM FE2 FE (II) ION HETNAM MN MANGANESE (II) ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NAG 3(C8 H15 N O6) FORMUL 3 GOL 4(C3 H8 O3) FORMUL 7 AKG C5 H6 O5 FORMUL 8 FE2 FE 2+ FORMUL 9 MN 2(MN 2+) FORMUL 12 HOH *263(H2 O) HELIX 1 AA1 ASN A 35 GLU A 37 5 3 HELIX 2 AA2 THR A 49 PHE A 62 1 14 HELIX 3 AA3 GLY A 87 GLU A 98 1 12 HELIX 4 AA4 LYS A 99 ALA A 101 5 3 HELIX 5 AA5 SER A 121 GLY A 133 1 13 HELIX 6 AA6 TRP A 148 GLN A 153 5 6 HELIX 7 AA7 ALA A 173 ARG A 181 1 9 HELIX 8 AA8 ASP A 190 LEU A 200 1 11 HELIX 9 AA9 ASP A 201 LEU A 208 1 8 HELIX 10 AB1 ALA A 225 ASP A 227 5 3 HELIX 11 AB2 THR A 258 ASN A 267 1 10 HELIX 12 AB3 GLY A 280 ASP A 285 1 6 HELIX 13 AB4 PHE A 310 LEU A 319 1 10 HELIX 14 AB5 PRO A 324 ASP A 326 5 3 HELIX 15 AB6 GLU A 336 PHE A 338 5 3 HELIX 16 AB7 HIS A 339 PHE A 354 1 16 HELIX 17 AB8 GLY A 361 ALA A 365 5 5 HELIX 18 AB9 SER A 367 GLN A 381 1 15 HELIX 19 AC1 GLN A 401 GLU A 409 1 9 HELIX 20 AC2 ASP A 443 GLN A 449 1 7 HELIX 21 AC3 GLY A 469 GLU A 475 1 7 HELIX 22 AC4 ASP A 488 LYS A 500 1 13 HELIX 23 AC5 HIS A 527 GLN A 532 5 6 HELIX 24 AC6 ASN A 536 ILE A 545 1 10 HELIX 25 AC7 ASN A 548 GLY A 555 1 8 HELIX 26 AC8 SER A 573 GLY A 588 1 16 HELIX 27 AC9 MET A 614 GLY A 618 1 5 HELIX 28 AD1 TYR A 619 TYR A 630 1 12 HELIX 29 AD2 TYR A 630 PHE A 639 1 10 HELIX 30 AD3 ARG A 695 ASP A 697 5 3 SHEET 1 AA1 6 VAL A 66 LEU A 69 0 SHEET 2 AA1 6 LEU A 39 VAL A 44 1 N VAL A 41 O ARG A 67 SHEET 3 AA1 6 ILE A 107 VAL A 111 1 O MET A 109 N ILE A 42 SHEET 4 AA1 6 PHE A 163 PHE A 172 -1 O GLY A 171 N ILE A 108 SHEET 5 AA1 6 LEU A 136 GLU A 141 -1 N LEU A 137 O ILE A 170 SHEET 6 AA1 6 LEU A 210 ASP A 213 1 O ASN A 211 N PHE A 138 SHEET 1 AA2 3 VAL A 116 LEU A 118 0 SHEET 2 AA2 3 VAL A 251 HIS A 253 -1 O VAL A 252 N ILE A 117 SHEET 3 AA2 3 PHE A 219 ASN A 221 1 N GLN A 220 O HIS A 253 SHEET 1 AA3 2 VAL A 229 PHE A 233 0 SHEET 2 AA3 2 VAL A 238 ASN A 242 -1 O ARG A 239 N LYS A 232 SHEET 1 AA4 2 TRP A 273 THR A 274 0 SHEET 2 AA4 2 GLY A 278 CYS A 279 -1 O GLY A 278 N THR A 274 SHEET 1 AA5 8 ALA A 356 VAL A 360 0 SHEET 2 AA5 8 VAL A 328 ASN A 334 1 N LEU A 330 O ALA A 356 SHEET 3 AA5 8 VAL A 298 VAL A 304 1 N LEU A 300 O PHE A 331 SHEET 4 AA5 8 PHE A 387 ASP A 392 1 O PHE A 389 N ALA A 301 SHEET 5 AA5 8 ALA A 464 ARG A 468 -1 O ILE A 467 N TYR A 388 SHEET 6 AA5 8 VAL A 413 PRO A 416 -1 N ILE A 414 O VAL A 466 SHEET 7 AA5 8 LEU A 504 SER A 507 1 O SER A 507 N ALA A 415 SHEET 8 AA5 8 VAL A 455 VAL A 458 -1 N TRP A 456 O LEU A 506 SHEET 1 AA6 3 ALA A 395 LEU A 397 0 SHEET 2 AA6 3 GLY A 513 LEU A 515 -1 O ARG A 514 N VAL A 396 SHEET 3 AA6 3 LEU A 418 ARG A 420 1 N SER A 419 O LEU A 515 SHEET 1 AA7 2 PHE A 428 TRP A 429 0 SHEET 2 AA7 2 TYR A 460 ILE A 461 -1 O TYR A 460 N TRP A 429 SHEET 1 AA8 2 ALA A 431 LEU A 432 0 SHEET 2 AA8 2 TYR A 438 ALA A 439 -1 O ALA A 439 N ALA A 431 SHEET 1 AA9 7 GLU A 560 CYS A 563 0 SHEET 2 AA9 7 VAL A 566 PRO A 570 -1 O TRP A 568 N GLU A 560 SHEET 3 AA9 7 TRP A 707 PRO A 712 -1 O LEU A 710 N TYR A 567 SHEET 4 AA9 7 PHE A 673 ALA A 678 -1 N THR A 674 O HIS A 711 SHEET 5 AA9 7 ARG A 729 VAL A 736 -1 O MET A 732 N VAL A 677 SHEET 6 AA9 7 ALA A 648 TYR A 656 -1 N TYR A 656 O ARG A 729 SHEET 7 AA9 7 ASP A 611 HIS A 613 -1 N ILE A 612 O VAL A 653 SHEET 1 AB1 5 ARG A 599 LEU A 600 0 SHEET 2 AB1 5 LEU A 664 ASP A 669 -1 O HIS A 668 N LEU A 600 SHEET 3 AB1 5 HIS A 719 GLY A 721 -1 O GLY A 721 N LEU A 664 SHEET 4 AB1 5 CYS A 691 PHE A 693 -1 N ARG A 692 O GLU A 720 SHEET 5 AB1 5 CYS A 698 ILE A 700 -1 O ILE A 700 N CYS A 691 SHEET 1 AB2 2 TYR A 686 GLY A 688 0 SHEET 2 AB2 2 THR A 724 GLY A 727 -1 O TRP A 726 N GLU A 687 SSBOND 1 CYS A 279 CYS A 282 1555 1555 2.06 SSBOND 2 CYS A 379 CYS A 385 1555 1555 2.04 SSBOND 3 CYS A 563 CYS A 698 1555 1555 2.04 LINK ND2 ASN A 63 C1 NAG A 809 1555 1555 1.44 LINK ND2 ASN A 548 C1 NAG B 1 1555 1555 1.45 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.44 LINK OD2 ASP A 112 MN MN A 807 1555 1555 2.38 LINK OD1 ASP A 115 MN MN A 807 1555 1555 2.36 LINK OD2 ASP A 115 MN MN A 807 1555 1555 2.28 LINK NE2 HIS A 253 MN MN A 807 1555 1555 2.32 LINK OD2 ASP A 597 MN MN A 808 1555 1555 1.85 LINK OD1 ASP A 611 MN MN A 808 1555 1555 2.47 LINK OD2 ASP A 611 MN MN A 808 1555 1555 1.96 LINK NE2 HIS A 667 FE FE2 A 806 1555 1555 2.19 LINK OD1 ASP A 669 FE FE2 A 806 1555 1555 1.95 LINK NE2 HIS A 719 FE FE2 A 806 1555 1555 2.02 LINK O2 AKG A 805 FE FE2 A 806 1555 1555 2.29 LINK O5 AKG A 805 FE FE2 A 806 1555 1555 2.22 LINK MN MN A 807 O HOH A1032 1555 1555 2.36 LINK MN MN A 807 O HOH A1137 1555 1555 2.47 LINK MN MN A 808 O HOH A1007 1555 1555 2.58 CISPEP 1 TRP A 145 PRO A 146 0 -0.27 CISPEP 2 VAL A 269 PRO A 270 0 -1.20 CRYST1 97.270 99.949 225.138 90.00 90.00 90.00 C 2 2 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 0.010281 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010005 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004442 0.00000