HEADER TRANSFERASE 11-NOV-19 6TE3 TITLE CRYSTAL STRUCTURE OF FULL-LENGTH HUMAN LYSYL HYDROXYLASE LH3 - TITLE 2 COCRYSTAL WITH FE2+, MN2+, UDP 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: 1.14.11.4,2.4.1.50,2.4.1.66; 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_COMMON: HUMAN; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 9606; SOURCE 9 EXPRESSION_SYSTEM_CELL_LINE: HEK293F; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PUPE.106.08 KEYWDS COLLAGEN, LYSYL HYDROXYLASE, HYDROXYLYSINE, GALACTOSYLTRANSFERASE, KEYWDS 2 GLUCOSYLTRANSFERASE, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.CHIAPPARINO,F.DE GIORGI,L.SCIETTI,S.FARAVELLI,T.ROSCIOLI,F.FORNERIS REVDAT 3 07-FEB-24 6TE3 1 REMARK REVDAT 2 19-JUL-23 6TE3 1 JRNL REVDAT 1 19-MAY-21 6TE3 0 JRNL AUTH D.MATTOTEIA,A.CHIAPPARINO,M.FUMAGALLI,M.DE MARCO, JRNL AUTH 2 F.DE GIORGI,L.NEGRO,A.PINNOLA,S.FARAVELLI,T.ROSCIOLI, JRNL AUTH 3 L.SCIETTI,F.FORNERIS JRNL TITL IDENTIFICATION OF REGULATORY MOLECULAR 'HOT SPOTS' FOR JRNL TITL 2 LH/PLOD COLLAGEN GLYCOSYLTRANSFERASE ACTIVITY JRNL REF INT J MOL SCI 2023 JRNL REFN ESSN 1422-0067 JRNL DOI 10.3390/IJMS241311213 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3549 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.84 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 62.5 REMARK 3 NUMBER OF REFLECTIONS : 30657 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.360 REMARK 3 FREE R VALUE TEST SET COUNT : 1642 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 48.8300 - 5.2600 1.00 4032 245 0.1756 0.2140 REMARK 3 2 5.2600 - 4.1800 1.00 3917 223 0.1449 0.2062 REMARK 3 3 4.1800 - 3.6500 0.99 3843 229 0.1717 0.2170 REMARK 3 4 3.6500 - 3.3200 0.89 3428 186 0.1922 0.2570 REMARK 3 5 3.3200 - 3.0800 0.78 2989 183 0.2337 0.2536 REMARK 3 6 3.0800 - 2.9000 0.66 2530 162 0.2445 0.3481 REMARK 3 7 2.9000 - 2.7500 0.56 2182 97 0.2554 0.3307 REMARK 3 8 2.7500 - 2.6300 0.47 1806 96 0.2723 0.3311 REMARK 3 9 2.6300 - 2.5300 0.38 1453 68 0.2737 0.3356 REMARK 3 10 2.5300 - 2.4400 0.30 1145 67 0.2775 0.2887 REMARK 3 11 2.4400 - 2.3700 0.25 945 60 0.2564 0.3214 REMARK 3 12 2.3700 - 2.3000 0.19 745 26 0.2538 0.2931 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) : 0.268 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.017 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.46 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 35.83 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 : 0.004 5880 REMARK 3 ANGLE : 0.618 7986 REMARK 3 CHIRALITY : 0.044 835 REMARK 3 PLANARITY : 0.005 1044 REMARK 3 DIHEDRAL : 16.494 3483 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 6 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 33 THROUGH 100 ) REMARK 3 ORIGIN FOR THE GROUP (A): 70.5582 30.7939 146.7644 REMARK 3 T TENSOR REMARK 3 T11: 0.2963 T22: 0.1551 REMARK 3 T33: 0.1442 T12: -0.0065 REMARK 3 T13: 0.0265 T23: -0.0030 REMARK 3 L TENSOR REMARK 3 L11: 0.0640 L22: 0.0173 REMARK 3 L33: 0.0418 L12: -0.0134 REMARK 3 L13: 0.0484 L23: -0.0019 REMARK 3 S TENSOR REMARK 3 S11: -0.1451 S12: 0.1748 S13: -0.0163 REMARK 3 S21: -0.0979 S22: -0.0165 S23: -0.0982 REMARK 3 S31: -0.1948 S32: 0.0400 S33: -0.0099 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 101 THROUGH 277 ) REMARK 3 ORIGIN FOR THE GROUP (A): 58.7583 22.0743 148.6917 REMARK 3 T TENSOR REMARK 3 T11: 0.0416 T22: 0.2449 REMARK 3 T33: 0.1293 T12: 0.1301 REMARK 3 T13: -0.0762 T23: -0.0400 REMARK 3 L TENSOR REMARK 3 L11: 0.1244 L22: 0.0757 REMARK 3 L33: 0.2279 L12: 0.0536 REMARK 3 L13: -0.0443 L23: 0.0911 REMARK 3 S TENSOR REMARK 3 S11: 0.0332 S12: 0.1278 S13: -0.0678 REMARK 3 S21: -0.1260 S22: -0.0700 S23: -0.0629 REMARK 3 S31: -0.1883 S32: -0.3238 S33: 0.0240 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 278 THROUGH 392 ) REMARK 3 ORIGIN FOR THE GROUP (A): 76.5850 41.6954 188.3409 REMARK 3 T TENSOR REMARK 3 T11: 0.1291 T22: 0.1274 REMARK 3 T33: 0.1951 T12: -0.0536 REMARK 3 T13: -0.0753 T23: -0.0033 REMARK 3 L TENSOR REMARK 3 L11: 0.0928 L22: 0.1138 REMARK 3 L33: 0.1766 L12: 0.0724 REMARK 3 L13: -0.1112 L23: -0.1369 REMARK 3 S TENSOR REMARK 3 S11: 0.1118 S12: -0.0512 S13: 0.0778 REMARK 3 S21: 0.1787 S22: -0.0626 S23: -0.0662 REMARK 3 S31: -0.0887 S32: 0.0498 S33: 0.0125 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 393 THROUGH 527 ) REMARK 3 ORIGIN FOR THE GROUP (A): 68.7256 30.4076 180.7057 REMARK 3 T TENSOR REMARK 3 T11: 0.1313 T22: 0.0956 REMARK 3 T33: 0.1740 T12: -0.0041 REMARK 3 T13: -0.0115 T23: 0.0198 REMARK 3 L TENSOR REMARK 3 L11: 0.0456 L22: 0.0887 REMARK 3 L33: 0.0990 L12: 0.0496 REMARK 3 L13: 0.0207 L23: 0.0557 REMARK 3 S TENSOR REMARK 3 S11: -0.0040 S12: -0.0248 S13: 0.0071 REMARK 3 S21: 0.0621 S22: 0.0199 S23: -0.0140 REMARK 3 S31: 0.0735 S32: -0.0680 S33: 0.0179 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 528 THROUGH 607 ) REMARK 3 ORIGIN FOR THE GROUP (A): 77.1732 19.8352 216.4350 REMARK 3 T TENSOR REMARK 3 T11: 0.2945 T22: 0.1711 REMARK 3 T33: 0.0745 T12: -0.0936 REMARK 3 T13: -0.0005 T23: 0.0467 REMARK 3 L TENSOR REMARK 3 L11: 1.5031 L22: 0.8711 REMARK 3 L33: 0.6273 L12: -0.5703 REMARK 3 L13: -0.0549 L23: 0.3964 REMARK 3 S TENSOR REMARK 3 S11: -0.0304 S12: -0.1390 S13: -0.0422 REMARK 3 S21: 0.0892 S22: 0.0129 S23: 0.0671 REMARK 3 S31: -0.0144 S32: 0.0745 S33: -0.0189 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 608 THROUGH 738 ) REMARK 3 ORIGIN FOR THE GROUP (A): 78.5146 16.0007 223.6752 REMARK 3 T TENSOR REMARK 3 T11: 0.3031 T22: 0.2020 REMARK 3 T33: 0.1365 T12: -0.0565 REMARK 3 T13: -0.0441 T23: 0.0522 REMARK 3 L TENSOR REMARK 3 L11: 0.0598 L22: 0.0757 REMARK 3 L33: 0.0443 L12: -0.0534 REMARK 3 L13: -0.0490 L23: 0.0222 REMARK 3 S TENSOR REMARK 3 S11: -0.0948 S12: 0.0637 S13: 0.0329 REMARK 3 S21: 0.1268 S22: -0.0117 S23: 0.0216 REMARK 3 S31: 0.0011 S32: 0.0417 S33: -0.0120 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 6TE3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 11-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1292105327. 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 : STARANISO, AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48288 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 48.840 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.11800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.80 REMARK 200 R MERGE FOR SHELL (I) : 1.47600 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 6FXM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.31 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 600 MM SODIUM FORMATE, 12% PGA-LM, 100 REMARK 280 MM HEPES/NAOH, 500 MM FECL2, 500 MM MNCL2, 1 MM UDP, PH 7.8, REMARK 280 VAPOR DIFFUSION, 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 112.60400 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 112.60400 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 48.49750 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.01750 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 48.49750 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.01750 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 112.60400 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 48.49750 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 50.01750 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 112.60400 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 48.49750 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 50.01750 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5610 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 58070 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 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 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 450.41600 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 902 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 990 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 GLY A 86 REMARK 465 ARG A 287 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 ALA A 739 REMARK 465 ALA A 740 REMARK 465 ALA A 741 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 LYS A 184 51.05 -141.45 REMARK 500 TYR A 185 -162.72 -127.24 REMARK 500 GLN A 284 -116.24 52.58 REMARK 500 GLN A 463 -29.91 72.99 REMARK 500 PRO A 564 -71.59 -39.09 REMARK 500 LEU A 571 -58.86 -127.20 REMARK 500 GLU A 660 -101.54 -104.37 REMARK 500 LEU A 715 -63.94 68.42 REMARK 500 HIS A 717 56.78 -113.35 REMARK 500 TYR A 718 109.83 -49.79 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 106.8 REMARK 620 3 ASP A 115 OD2 164.8 58.0 REMARK 620 4 HIS A 253 NE2 87.9 86.1 89.7 REMARK 620 5 HOH A1031 O 107.7 144.9 87.3 89.0 REMARK 620 N 1 2 3 4 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 595 NE2 REMARK 620 2 ASP A 597 OD1 116.9 REMARK 620 3 ASP A 611 OD1 61.5 156.7 REMARK 620 4 ASP A 611 OD2 72.4 106.7 50.0 REMARK 620 5 HIS A 613 NE2 119.1 100.6 99.6 140.5 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 A 805 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 667 NE2 REMARK 620 2 ASP A 669 OD1 114.4 REMARK 620 3 HIS A 719 NE2 72.6 134.1 REMARK 620 4 AKG A 804 O2 78.6 122.7 103.2 REMARK 620 5 AKG A 804 O5 75.2 160.5 29.7 74.9 REMARK 620 N 1 2 3 4 DBREF 6TE3 A 25 738 UNP O60568 PLOD3_HUMAN 25 738 SEQADV 6TE3 SER A 24 UNP O60568 EXPRESSION TAG SEQADV 6TE3 ALA A 739 UNP O60568 EXPRESSION TAG SEQADV 6TE3 ALA A 740 UNP O60568 EXPRESSION TAG SEQADV 6TE3 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 AKG A 804 10 HET FE2 A 805 1 HET FE2 A 806 1 HET MN A 807 1 HET NAG A 808 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 NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NAG 3(C8 H15 N O6) FORMUL 3 GOL 3(C3 H8 O3) FORMUL 6 AKG C5 H6 O5 FORMUL 7 FE2 2(FE 2+) FORMUL 9 MN MN 2+ FORMUL 11 HOH *155(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 GLN A 88 GLU A 98 1 11 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 GLU A 147 TYR A 154 5 8 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 SER A 209 1 9 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 PHE A 310 LEU A 318 1 9 HELIX 13 AB4 LEU A 319 LEU A 321 5 3 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 GLU A 554 1 7 HELIX 26 AC8 SER A 573 GLY A 588 1 16 HELIX 27 AC9 TYR A 619 TYR A 630 1 12 HELIX 28 AD1 TYR A 630 PHE A 639 1 10 HELIX 29 AD2 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 HIS A 505 SER A 507 1 O SER A 507 N ALA A 415 SHEET 8 AA5 8 VAL A 455 ASN A 457 -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 PHE A 652 O VAL A 733 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 2.03 SSBOND 2 CYS A 379 CYS A 385 1555 1555 2.03 SSBOND 3 CYS A 563 CYS A 698 1555 1555 2.03 LINK ND2 ASN A 63 C1 NAG A 808 1555 1555 1.44 LINK ND2 ASN A 548 C1 NAG B 1 1555 1555 1.44 LINK NE2 HIS A 719 O5 AKG A 804 1555 1555 1.30 LINK O4 NAG B 1 C1 NAG B 2 1555 1555 1.38 LINK OD2 ASP A 112 MN MN A 807 1555 1555 2.38 LINK OD1 ASP A 115 MN MN A 807 1555 1555 2.43 LINK OD2 ASP A 115 MN MN A 807 1555 1555 2.03 LINK NE2 HIS A 253 MN MN A 807 1555 1555 2.46 LINK NE2 HIS A 595 FE FE2 A 806 1555 1555 2.47 LINK OD1 ASP A 597 FE FE2 A 806 1555 1555 2.67 LINK OD1 ASP A 611 FE FE2 A 806 1555 1555 2.65 LINK OD2 ASP A 611 FE FE2 A 806 1555 1555 2.56 LINK NE2 HIS A 613 FE FE2 A 806 1555 1555 2.69 LINK NE2 HIS A 667 FE FE2 A 805 1555 1555 2.68 LINK OD1 ASP A 669 FE FE2 A 805 1555 1555 2.28 LINK NE2 HIS A 719 FE FE2 A 805 1555 1555 2.61 LINK O2 AKG A 804 FE FE2 A 805 1555 1555 2.41 LINK O5 AKG A 804 FE FE2 A 805 1555 1555 2.44 LINK MN MN A 807 O HOH A1031 1555 1555 2.72 CISPEP 1 TRP A 145 PRO A 146 0 0.32 CISPEP 2 VAL A 269 PRO A 270 0 -3.60 CRYST1 96.995 100.035 225.208 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 0.010310 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009997 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004440 0.00000