HEADER TRANSFERASE 11-NOV-19 6TEC TITLE CRYSTAL STRUCTURE OF FULL-LENGTH HUMAN LYSYL HYDROXYLASE LH3 - TITLE 2 COCRYSTAL WITH FE2+, MN2+, UDP-XYLOSE 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; COMPND 7 OTHER_DETAILS: FIRST SER RESIDUE AND LAST THREE ALA RESIDUES WERE COMPND 8 INTRODUCED BY MOLECULAR CLONING 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 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 6TEC 1 REMARK REVDAT 2 19-JUL-23 6TEC 1 JRNL REVDAT 1 19-MAY-21 6TEC 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. 2.40 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) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.79 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 63.2 REMARK 3 NUMBER OF REFLECTIONS : 27202 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.216 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.780 REMARK 3 FREE R VALUE TEST SET COUNT : 1300 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 48.7900 - 4.9900 0.99 4693 252 0.1651 0.1848 REMARK 3 2 4.9900 - 3.9600 1.00 4614 232 0.1425 0.1685 REMARK 3 3 3.9600 - 3.4600 1.00 4549 214 0.1748 0.2230 REMARK 3 4 3.4600 - 3.1500 0.93 4226 197 0.2075 0.2515 REMARK 3 5 3.1500 - 2.9200 0.71 3244 154 0.2519 0.2856 REMARK 3 6 2.9200 - 2.7500 0.49 2226 115 0.2619 0.2900 REMARK 3 7 2.7500 - 2.6100 0.27 1218 72 0.2709 0.2715 REMARK 3 8 2.6100 - 2.5000 0.15 673 36 0.2861 0.2626 REMARK 3 9 2.5000 - 2.4000 0.10 459 28 0.2415 0.2706 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) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.710 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 26.48 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.49 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 : 0.002 6026 REMARK 3 ANGLE : 0.515 8191 REMARK 3 CHIRALITY : 0.042 858 REMARK 3 PLANARITY : 0.004 1067 REMARK 3 DIHEDRAL : 16.946 3545 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 132 ) REMARK 3 ORIGIN FOR THE GROUP (A): 67.9784 29.0520 145.9899 REMARK 3 T TENSOR REMARK 3 T11: 0.0665 T22: 0.0702 REMARK 3 T33: 0.0325 T12: 0.0240 REMARK 3 T13: 0.0050 T23: 0.0086 REMARK 3 L TENSOR REMARK 3 L11: 0.1596 L22: 0.0600 REMARK 3 L33: 0.0787 L12: 0.0426 REMARK 3 L13: 0.0439 L23: 0.0380 REMARK 3 S TENSOR REMARK 3 S11: 0.0207 S12: 0.0916 S13: -0.0157 REMARK 3 S21: -0.0599 S22: -0.0195 S23: -0.0059 REMARK 3 S31: -0.0915 S32: 0.0050 S33: 0.0191 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 133 THROUGH 277 ) REMARK 3 ORIGIN FOR THE GROUP (A): 57.0517 22.0744 149.0830 REMARK 3 T TENSOR REMARK 3 T11: 0.0682 T22: 0.0753 REMARK 3 T33: 0.0539 T12: 0.0532 REMARK 3 T13: -0.0533 T23: -0.0370 REMARK 3 L TENSOR REMARK 3 L11: 0.0253 L22: 0.0022 REMARK 3 L33: 0.1076 L12: 0.0071 REMARK 3 L13: -0.0517 L23: -0.0139 REMARK 3 S TENSOR REMARK 3 S11: 0.0214 S12: 0.0580 S13: -0.0024 REMARK 3 S21: -0.0760 S22: -0.0463 S23: 0.0653 REMARK 3 S31: -0.0568 S32: -0.1039 S33: 0.0687 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 278 THROUGH 392 ) REMARK 3 ORIGIN FOR THE GROUP (A): 77.0510 41.6552 187.1645 REMARK 3 T TENSOR REMARK 3 T11: 0.0674 T22: 0.0415 REMARK 3 T33: 0.1014 T12: -0.0300 REMARK 3 T13: -0.0298 T23: 0.0063 REMARK 3 L TENSOR REMARK 3 L11: 0.0217 L22: 0.0586 REMARK 3 L33: 0.0063 L12: 0.0084 REMARK 3 L13: -0.0113 L23: -0.0098 REMARK 3 S TENSOR REMARK 3 S11: 0.0352 S12: -0.0359 S13: 0.0079 REMARK 3 S21: 0.0749 S22: -0.0341 S23: -0.0384 REMARK 3 S31: 0.0115 S32: 0.0084 S33: 0.0047 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 393 THROUGH 500 ) REMARK 3 ORIGIN FOR THE GROUP (A): 68.6986 30.8367 177.0690 REMARK 3 T TENSOR REMARK 3 T11: 0.0228 T22: 0.0307 REMARK 3 T33: 0.0849 T12: -0.0129 REMARK 3 T13: -0.0112 T23: 0.0185 REMARK 3 L TENSOR REMARK 3 L11: 0.0151 L22: 0.0007 REMARK 3 L33: 0.0357 L12: -0.0015 REMARK 3 L13: -0.0225 L23: 0.0032 REMARK 3 S TENSOR REMARK 3 S11: -0.0011 S12: 0.0123 S13: -0.0002 REMARK 3 S21: 0.0001 S22: 0.0110 S23: 0.0084 REMARK 3 S31: 0.0167 S32: -0.0298 S33: 0.0323 REMARK 3 TLS GROUP : 5 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 501 THROUGH 536 ) REMARK 3 ORIGIN FOR THE GROUP (A): 70.1682 27.7060 193.0548 REMARK 3 T TENSOR REMARK 3 T11: 0.1013 T22: 0.0732 REMARK 3 T33: 0.0698 T12: -0.0195 REMARK 3 T13: -0.0180 T23: 0.0432 REMARK 3 L TENSOR REMARK 3 L11: 0.0131 L22: 0.0217 REMARK 3 L33: 0.0069 L12: 0.0160 REMARK 3 L13: -0.0074 L23: -0.0118 REMARK 3 S TENSOR REMARK 3 S11: 0.0312 S12: -0.0330 S13: -0.0078 REMARK 3 S21: 0.0566 S22: -0.0064 S23: 0.0028 REMARK 3 S31: 0.0062 S32: -0.0076 S33: 0.0074 REMARK 3 TLS GROUP : 6 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 537 THROUGH 738 ) REMARK 3 ORIGIN FOR THE GROUP (A): 79.1333 17.0723 220.4093 REMARK 3 T TENSOR REMARK 3 T11: 0.2263 T22: 0.1475 REMARK 3 T33: 0.0712 T12: -0.0537 REMARK 3 T13: -0.0270 T23: 0.0483 REMARK 3 L TENSOR REMARK 3 L11: 0.0066 L22: 0.0079 REMARK 3 L33: 0.0242 L12: -0.0010 REMARK 3 L13: -0.0074 L23: -0.0093 REMARK 3 S TENSOR REMARK 3 S11: -0.0099 S12: -0.0176 S13: 0.0076 REMARK 3 S21: 0.0606 S22: -0.0320 S23: -0.0235 REMARK 3 S31: -0.0138 S32: 0.0917 S33: -0.0325 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 6TEC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1292105337. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-OCT-18 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 : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.873 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS, STARANISO REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 43005 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 5.500 REMARK 200 R MERGE (I) : 0.20900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 1.83100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 5.700 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: 6FXK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.42 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.36 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 600 MM SODIUM FORMATE, 12% PGA-LM, 100 REMARK 280 MM HEPES/NAOH, 500 UM FECL2, 500 UM MNCL2, 1 MM UDP-XYLOSE, PH REMARK 280 7.8, VAPOR DIFFUSION, HANGING 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 111.98000 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 111.98000 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 48.63200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 49.99350 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 48.63200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 49.99350 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 111.98000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 48.63200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 49.99350 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 111.98000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 48.63200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 49.99350 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: 7670 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 58850 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 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 447.92000 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 952 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 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 30.90 -145.50 REMARK 500 ALA A 225 27.63 -144.36 REMARK 500 PRO A 257 36.32 -89.40 REMARK 500 ASP A 435 35.21 -97.87 REMARK 500 GLN A 463 -35.48 71.85 REMARK 500 LEU A 571 -58.30 -128.49 REMARK 500 ALA A 601 -158.43 -105.83 REMARK 500 GLU A 660 -103.32 -124.44 REMARK 500 LEU A 715 -57.33 76.90 REMARK 500 HIS A 717 57.42 -112.58 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 805 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 112 OD2 REMARK 620 2 ASP A 115 OD1 119.6 REMARK 620 3 ASP A 115 OD2 171.2 54.1 REMARK 620 4 HIS A 253 NE2 91.3 96.1 83.7 REMARK 620 5 UDX A 801 O1B 106.3 130.9 81.7 99.5 REMARK 620 6 UDX A 801 O1A 108.1 71.4 76.6 160.2 79.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 A 804 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 595 NE2 REMARK 620 2 ASP A 597 OD1 132.9 REMARK 620 3 ASP A 597 OD2 91.9 49.6 REMARK 620 4 ASP A 611 OD1 68.9 144.7 114.2 REMARK 620 5 ASP A 611 OD2 95.5 96.4 72.5 49.6 REMARK 620 6 HIS A 613 NE2 110.9 95.9 144.1 100.0 129.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 FE2 A 803 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 667 NE2 REMARK 620 2 ASP A 669 OD1 91.4 REMARK 620 3 ASP A 669 OD2 131.9 50.6 REMARK 620 4 HIS A 719 NE2 92.4 103.1 73.2 REMARK 620 5 AKG A 802 O2 80.5 105.6 131.8 150.5 REMARK 620 6 AKG A 802 O5 94.3 173.4 126.2 80.1 72.1 REMARK 620 N 1 2 3 4 5 DBREF 6TEC A 25 738 UNP O60568 PLOD3_HUMAN 25 738 SEQADV 6TEC SER A 24 UNP O60568 EXPRESSION TAG SEQADV 6TEC ALA A 739 UNP O60568 EXPRESSION TAG SEQADV 6TEC ALA A 740 UNP O60568 EXPRESSION TAG SEQADV 6TEC 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 UDX A 801 34 HET AKG A 802 10 HET FE2 A 803 1 HET FE2 A 804 1 HET MN A 805 1 HET NAG A 806 14 HET EDO A 809 4 HET EDO A 810 4 HET EDO A 811 4 HET EDO A 812 4 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM UDX URIDINE-5'-DIPHOSPHATE-XYLOPYRANOSE HETNAM AKG 2-OXOGLUTARIC ACID HETNAM FE2 FE (II) ION HETNAM MN MANGANESE (II) ION HETNAM EDO 1,2-ETHANEDIOL 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 UDX UDP-ALPHA-D-XYLOPYRANOSE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 NAG 3(C8 H15 N O6) FORMUL 3 UDX C14 H22 N2 O16 P2 FORMUL 4 AKG C5 H6 O5 FORMUL 5 FE2 2(FE 2+) FORMUL 7 MN MN 2+ FORMUL 9 EDO 4(C2 H6 O2) FORMUL 13 HOH *159(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 86 GLU A 98 1 13 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 GLN A 153 5 7 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 PHE A 310 LEU A 319 1 10 HELIX 13 AB4 PRO A 324 ASP A 326 5 3 HELIX 14 AB5 GLU A 336 PHE A 338 5 3 HELIX 15 AB6 HIS A 339 PHE A 354 1 16 HELIX 16 AB7 GLY A 361 ALA A 365 5 5 HELIX 17 AB8 SER A 367 GLN A 381 1 15 HELIX 18 AB9 GLN A 401 GLU A 409 1 9 HELIX 19 AC1 ASP A 443 GLN A 449 1 7 HELIX 20 AC2 GLY A 469 GLU A 475 1 7 HELIX 21 AC3 ASP A 488 LYS A 500 1 13 HELIX 22 AC4 HIS A 527 GLN A 532 5 6 HELIX 23 AC5 ASN A 536 ILE A 545 1 10 HELIX 24 AC6 ASN A 548 GLU A 554 1 7 HELIX 25 AC7 SER A 573 GLY A 588 1 16 HELIX 26 AC8 MET A 614 GLY A 618 1 5 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 THR A 43 O LEU A 69 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 VAL A 302 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 ALA A 708 N PHE A 569 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 2.04 SSBOND 3 CYS A 563 CYS A 698 1555 1555 2.03 LINK ND2 ASN A 63 C1 NAG A 806 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 1.38 LINK OD2 ASP A 112 MN MN A 805 1555 1555 2.27 LINK OD1 ASP A 115 MN MN A 805 1555 1555 2.34 LINK OD2 ASP A 115 MN MN A 805 1555 1555 2.48 LINK NE2 HIS A 253 MN MN A 805 1555 1555 2.25 LINK NE2 HIS A 595 FE FE2 A 804 1555 1555 2.53 LINK OD1 ASP A 597 FE FE2 A 804 1555 1555 2.54 LINK OD2 ASP A 597 FE FE2 A 804 1555 1555 2.70 LINK OD1 ASP A 611 FE FE2 A 804 1555 1555 2.63 LINK OD2 ASP A 611 FE FE2 A 804 1555 1555 2.60 LINK NE2 HIS A 613 FE FE2 A 804 1555 1555 2.59 LINK NE2 HIS A 667 FE FE2 A 803 1555 1555 2.54 LINK OD1 ASP A 669 FE FE2 A 803 1555 1555 2.45 LINK OD2 ASP A 669 FE FE2 A 803 1555 1555 2.68 LINK NE2 HIS A 719 FE FE2 A 803 1555 1555 2.50 LINK O1B UDX A 801 MN MN A 805 1555 1555 1.92 LINK O1A UDX A 801 MN MN A 805 1555 1555 2.54 LINK O2 AKG A 802 FE FE2 A 803 1555 1555 2.53 LINK O5 AKG A 802 FE FE2 A 803 1555 1555 2.53 CISPEP 1 TRP A 145 PRO A 146 0 2.85 CISPEP 2 VAL A 269 PRO A 270 0 -3.26 CRYST1 97.264 99.987 223.960 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 0.010001 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004465 0.00000