HEADER SUGAR BINDING PROTEIN 18-SEP-14 4RDA TITLE X-RAY STRUCTURE OF THE AMYLOID PRECURSOR PROTEIN-LIKE PROTEIN 1 TITLE 2 (APLP1) E2 DOMAIN IN COMPLEX WITH A HEPARIN DODECASACCHARIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: AMYLOID-LIKE PROTEIN 1; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: E2 DOMAIN, UNP RESIDUES 292-494; COMPND 5 SYNONYM: APLP, APLP-1, C30; 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: APLP1; SOURCE 6 EXPRESSION_SYSTEM: PICHIA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922 KEYWDS HEPARAN SULFATE BINDING, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.O.DAHMS,M.E.THAN REVDAT 4 28-FEB-24 4RDA 1 REMARK HETSYN REVDAT 3 29-JUL-20 4RDA 1 COMPND REMARK SEQADV HETNAM REVDAT 3 2 1 LINK SITE ATOM REVDAT 2 18-MAR-15 4RDA 1 JRNL REVDAT 1 11-MAR-15 4RDA 0 JRNL AUTH S.O.DAHMS,M.C.MAYER,D.ROESER,G.MULTHAUP,M.E.THAN JRNL TITL INTERACTION OF THE AMYLOID PRECURSOR PROTEIN-LIKE PROTEIN 1 JRNL TITL 2 (APLP1) E2 DOMAIN WITH HEPARAN SULFATE INVOLVES TWO DISTINCT JRNL TITL 3 BINDING MODES. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 71 494 2015 JRNL REFN ISSN 0907-4449 JRNL PMID 25760599 JRNL DOI 10.1107/S1399004714027114 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.9_1692) 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 : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 36044 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.218 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.245 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1803 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 45.9923 - 5.8675 0.99 2818 149 0.1983 0.1846 REMARK 3 2 5.8675 - 4.6586 0.99 2677 141 0.1989 0.2393 REMARK 3 3 4.6586 - 4.0702 0.99 2656 140 0.1855 0.2278 REMARK 3 4 4.0702 - 3.6982 1.00 2637 139 0.1896 0.2024 REMARK 3 5 3.6982 - 3.4332 1.00 2645 139 0.2083 0.2429 REMARK 3 6 3.4332 - 3.2309 0.99 2636 139 0.2342 0.2966 REMARK 3 7 3.2309 - 3.0691 1.00 2603 136 0.2620 0.3452 REMARK 3 8 3.0691 - 2.9355 1.00 2636 139 0.2539 0.3135 REMARK 3 9 2.9355 - 2.8225 1.00 2607 137 0.2441 0.2708 REMARK 3 10 2.8225 - 2.7251 1.00 2611 138 0.2506 0.3111 REMARK 3 11 2.7251 - 2.6399 1.00 2606 137 0.2815 0.3181 REMARK 3 12 2.6399 - 2.5645 1.00 2581 136 0.2967 0.3004 REMARK 3 13 2.5645 - 2.4970 0.97 2528 133 0.3146 0.3558 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.340 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 27.380 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 : 0.004 3549 REMARK 3 ANGLE : 0.900 4818 REMARK 3 CHIRALITY : NULL 528 REMARK 3 PLANARITY : NULL 626 REMARK 3 DIHEDRAL : NULL 1379 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ( CHAIN A AND RESID 292:494 ) REMARK 3 ORIGIN FOR THE GROUP (A): 98.0139 105.6965 204.6024 REMARK 3 T TENSOR REMARK 3 T11: 0.4110 T22: 0.3587 REMARK 3 T33: 0.3891 T12: -0.0534 REMARK 3 T13: -0.0004 T23: -0.0099 REMARK 3 L TENSOR REMARK 3 L11: 0.3113 L22: 0.4826 REMARK 3 L33: 1.9161 L12: 0.0106 REMARK 3 L13: 0.0031 L23: -0.3745 REMARK 3 S TENSOR REMARK 3 S11: 0.0058 S12: 0.0540 S13: -0.0410 REMARK 3 S21: 0.0761 S22: -0.0228 S23: 0.0681 REMARK 3 S31: -0.2503 S32: 0.2192 S33: 0.0000 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: ( CHAIN B AND RESID 292:487 ) REMARK 3 ORIGIN FOR THE GROUP (A): 94.3141 86.4778 216.4666 REMARK 3 T TENSOR REMARK 3 T11: 0.3799 T22: 0.3337 REMARK 3 T33: 0.4274 T12: -0.1044 REMARK 3 T13: 0.0060 T23: 0.0043 REMARK 3 L TENSOR REMARK 3 L11: 0.1437 L22: 1.3036 REMARK 3 L33: 0.8164 L12: -0.4739 REMARK 3 L13: -0.2739 L23: -0.9884 REMARK 3 S TENSOR REMARK 3 S11: 0.1373 S12: -0.0182 S13: 0.0686 REMARK 3 S21: -0.0287 S22: 0.0116 S23: -0.1388 REMARK 3 S31: -0.0679 S32: -0.1486 S33: 0.1619 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: ( CHAIN A AND RESID 501:505 ) REMARK 3 ORIGIN FOR THE GROUP (A): 99.5804 99.0788 204.1129 REMARK 3 T TENSOR REMARK 3 T11: 1.1166 T22: 0.8002 REMARK 3 T33: 1.0546 T12: -0.0324 REMARK 3 T13: 0.0585 T23: 0.0022 REMARK 3 L TENSOR REMARK 3 L11: 0.0326 L22: 0.0558 REMARK 3 L33: 0.0281 L12: -0.0146 REMARK 3 L13: 0.0352 L23: -0.0211 REMARK 3 S TENSOR REMARK 3 S11: 0.2499 S12: 0.2635 S13: -0.4953 REMARK 3 S21: -0.2815 S22: -0.2716 S23: 0.7004 REMARK 3 S31: 0.3929 S32: 0.0143 S33: 0.0000 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: ( CHAIN B AND RESID 501:506 ) REMARK 3 ORIGIN FOR THE GROUP (A): 104.7770 84.2805 214.0486 REMARK 3 T TENSOR REMARK 3 T11: 1.4157 T22: 1.5117 REMARK 3 T33: 1.3677 T12: -0.1602 REMARK 3 T13: 0.3085 T23: 0.0333 REMARK 3 L TENSOR REMARK 3 L11: 0.0538 L22: 0.0174 REMARK 3 L33: 0.0458 L12: 0.0387 REMARK 3 L13: 0.0118 L23: -0.0263 REMARK 3 S TENSOR REMARK 3 S11: -0.3126 S12: -0.1588 S13: -0.2581 REMARK 3 S21: 0.3943 S22: -0.6276 S23: -0.3832 REMARK 3 S31: 0.2337 S32: 0.2295 S33: 0.0000 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 4RDA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-SEP-14. REMARK 100 THE DEPOSITION ID IS D_1000087202. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 17-JUN-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9184 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 36051 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.497 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.65 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.4 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.53800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.050 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 (%): 76.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 MM MES/NAOH 9.5% PEG20000, PH 6.2, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 69.49367 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 138.98733 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 138.98733 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 69.49367 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 300 REMARK: X, Y, Z 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: 8400 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -11.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 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 GLU A 286 REMARK 465 ALA A 287 REMARK 465 GLU A 288 REMARK 465 PHE A 289 REMARK 465 PRO A 290 REMARK 465 THR A 291 REMARK 465 LEU A 495 REMARK 465 GLU B 286 REMARK 465 ALA B 287 REMARK 465 GLU B 288 REMARK 465 PHE B 289 REMARK 465 PRO B 290 REMARK 465 THR B 291 REMARK 465 GLU B 488 REMARK 465 HIS B 489 REMARK 465 LEU B 490 REMARK 465 GLY B 491 REMARK 465 PRO B 492 REMARK 465 SER B 493 REMARK 465 GLU B 494 REMARK 465 LEU B 495 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 312 NE CZ NH1 NH2 REMARK 480 MET A 315 CE REMARK 480 GLU A 319 OE1 OE2 REMARK 480 ARG A 323 CZ NH1 NH2 REMARK 480 ARG A 330 NE CZ NH1 NH2 REMARK 480 MET A 334 CE REMARK 480 SER A 339 OG REMARK 480 LYS A 340 CG CD CE NZ REMARK 480 LYS A 344 CE NZ REMARK 480 GLU A 374 CD OE1 OE2 REMARK 480 LEU A 383 CD1 CD2 REMARK 480 GLN A 387 OE1 NE2 REMARK 480 GLN A 405 OE1 NE2 REMARK 480 LEU A 411 CD1 CD2 REMARK 480 ARG A 415 CD NE CZ NH1 NH2 REMARK 480 LYS A 422 NZ REMARK 480 ARG A 425 NH1 NH2 REMARK 480 GLU A 440 CG CD OE1 OE2 REMARK 480 LYS A 441 CD CE NZ REMARK 480 GLN A 443 OE1 NE2 REMARK 480 GLN A 444 CD OE1 NE2 REMARK 480 GLN A 448 CD OE1 NE2 REMARK 480 ASN A 470 OD1 ND2 REMARK 480 HIS A 472 CG ND1 CD2 CE1 NE2 REMARK 480 LEU A 473 CD1 CD2 REMARK 480 GLU A 483 OE1 OE2 REMARK 480 ILE B 296 CD1 REMARK 480 GLU B 308 OE1 OE2 REMARK 480 ARG B 312 CZ REMARK 480 ARG B 330 NH1 NH2 REMARK 480 LEU B 342 CD1 CD2 REMARK 480 LYS B 344 CE NZ REMARK 480 ASP B 346 CG OD1 OD2 REMARK 480 ARG B 347 NH1 NH2 REMARK 480 GLN B 348 CD OE1 NE2 REMARK 480 GLU B 352 CG CD OE1 OE2 REMARK 480 ILE B 357 CD1 REMARK 480 GLU B 374 OE1 OE2 REMARK 480 LEU B 383 CD1 CD2 REMARK 480 GLN B 405 OE1 NE2 REMARK 480 GLU B 407 CG CD OE1 OE2 REMARK 480 LEU B 411 CD1 CD2 REMARK 480 ARG B 414 CD NE CZ NH1 NH2 REMARK 480 ARG B 418 NE CZ NH1 NH2 REMARK 480 GLN B 443 OE1 NE2 REMARK 480 GLN B 448 OE1 NE2 REMARK 480 HIS B 472 CG ND1 CD2 CE1 NE2 REMARK 480 GLN B 475 CG CD OE1 NE2 REMARK 480 LEU B 477 CD1 CD2 REMARK 480 ARG B 478 CG CD NE CZ NH1 NH2 REMARK 480 PRO B 479 CB CG CD REMARK 480 ILE B 481 CG1 CG2 CD1 REMARK 480 GLN B 482 CG CD OE1 NE2 REMARK 480 GLU B 483 CG CD OE1 OE2 REMARK 480 LEU B 484 CG CD1 CD2 REMARK 480 HIS B 486 CG ND1 CD2 CE1 NE2 REMARK 480 SER B 487 OG 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 611 O HOH A 613 1.94 REMARK 500 O HOH A 609 O HOH A 611 1.96 REMARK 500 O HOH A 612 O HOH A 613 1.98 REMARK 500 O HOH A 602 O HOH A 609 2.03 REMARK 500 O HOH A 601 O HOH A 602 2.04 REMARK 500 O HOH A 610 O HOH A 611 2.04 REMARK 500 O HOH A 604 O HOH A 608 2.04 REMARK 500 O HOH A 614 O HOH A 615 2.07 REMARK 500 O HOH A 608 O HOH A 610 2.09 REMARK 500 O HOH A 601 O HOH A 604 2.11 REMARK 500 O HOH A 605 O HOH A 606 2.12 REMARK 500 O HOH A 607 O HOH A 608 2.13 REMARK 500 O HOH A 603 O HOH A 608 2.13 REMARK 500 O HOH A 606 O HOH A 607 2.14 REMARK 500 O HOH A 608 O HOH A 609 2.16 REMARK 500 OE1 GLU A 457 NH2 ARG B 330 2.17 REMARK 500 O HOH A 603 O HOH A 607 2.17 REMARK 500 O HOH A 601 O HOH A 609 2.19 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 ASP A 438 67.95 -161.63 REMARK 500 HIS B 486 35.27 -98.91 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 IDS D 1 REMARK 615 SGN D 2 REMARK 615 IDS D 3 REMARK 615 SGN D 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4RD9 RELATED DB: PDB DBREF 4RDA A 290 495 UNP P51693 APLP1_HUMAN 290 495 DBREF 4RDA B 290 495 UNP P51693 APLP1_HUMAN 290 495 SEQADV 4RDA GLU A 286 UNP P51693 CLONING ARTIFACT SEQADV 4RDA ALA A 287 UNP P51693 CLONING ARTIFACT SEQADV 4RDA GLU A 288 UNP P51693 CLONING ARTIFACT SEQADV 4RDA PHE A 289 UNP P51693 CLONING ARTIFACT SEQADV 4RDA GLU B 286 UNP P51693 CLONING ARTIFACT SEQADV 4RDA ALA B 287 UNP P51693 CLONING ARTIFACT SEQADV 4RDA GLU B 288 UNP P51693 CLONING ARTIFACT SEQADV 4RDA PHE B 289 UNP P51693 CLONING ARTIFACT SEQRES 1 A 210 GLU ALA GLU PHE PRO THR ASP GLY VAL ASP ILE TYR PHE SEQRES 2 A 210 GLY MET PRO GLY GLU ILE SER GLU HIS GLU GLY PHE LEU SEQRES 3 A 210 ARG ALA LYS MET ASP LEU GLU GLU ARG ARG MET ARG GLN SEQRES 4 A 210 ILE ASN GLU VAL MET ARG GLU TRP ALA MET ALA ASP ASN SEQRES 5 A 210 GLN SER LYS ASN LEU PRO LYS ALA ASP ARG GLN ALA LEU SEQRES 6 A 210 ASN GLU HIS PHE GLN SER ILE LEU GLN THR LEU GLU GLU SEQRES 7 A 210 GLN VAL SER GLY GLU ARG GLN ARG LEU VAL GLU THR HIS SEQRES 8 A 210 ALA THR ARG VAL ILE ALA LEU ILE ASN ASP GLN ARG ARG SEQRES 9 A 210 ALA ALA LEU GLU GLY PHE LEU ALA ALA LEU GLN ALA ASP SEQRES 10 A 210 PRO PRO GLN ALA GLU ARG VAL LEU LEU ALA LEU ARG ARG SEQRES 11 A 210 TYR LEU ARG ALA GLU GLN LYS GLU GLN ARG HIS THR LEU SEQRES 12 A 210 ARG HIS TYR GLN HIS VAL ALA ALA VAL ASP PRO GLU LYS SEQRES 13 A 210 ALA GLN GLN MET ARG PHE GLN VAL HIS THR HIS LEU GLN SEQRES 14 A 210 VAL ILE GLU GLU ARG VAL ASN GLN SER LEU GLY LEU LEU SEQRES 15 A 210 ASP GLN ASN PRO HIS LEU ALA GLN GLU LEU ARG PRO GLN SEQRES 16 A 210 ILE GLN GLU LEU LEU HIS SER GLU HIS LEU GLY PRO SER SEQRES 17 A 210 GLU LEU SEQRES 1 B 210 GLU ALA GLU PHE PRO THR ASP GLY VAL ASP ILE TYR PHE SEQRES 2 B 210 GLY MET PRO GLY GLU ILE SER GLU HIS GLU GLY PHE LEU SEQRES 3 B 210 ARG ALA LYS MET ASP LEU GLU GLU ARG ARG MET ARG GLN SEQRES 4 B 210 ILE ASN GLU VAL MET ARG GLU TRP ALA MET ALA ASP ASN SEQRES 5 B 210 GLN SER LYS ASN LEU PRO LYS ALA ASP ARG GLN ALA LEU SEQRES 6 B 210 ASN GLU HIS PHE GLN SER ILE LEU GLN THR LEU GLU GLU SEQRES 7 B 210 GLN VAL SER GLY GLU ARG GLN ARG LEU VAL GLU THR HIS SEQRES 8 B 210 ALA THR ARG VAL ILE ALA LEU ILE ASN ASP GLN ARG ARG SEQRES 9 B 210 ALA ALA LEU GLU GLY PHE LEU ALA ALA LEU GLN ALA ASP SEQRES 10 B 210 PRO PRO GLN ALA GLU ARG VAL LEU LEU ALA LEU ARG ARG SEQRES 11 B 210 TYR LEU ARG ALA GLU GLN LYS GLU GLN ARG HIS THR LEU SEQRES 12 B 210 ARG HIS TYR GLN HIS VAL ALA ALA VAL ASP PRO GLU LYS SEQRES 13 B 210 ALA GLN GLN MET ARG PHE GLN VAL HIS THR HIS LEU GLN SEQRES 14 B 210 VAL ILE GLU GLU ARG VAL ASN GLN SER LEU GLY LEU LEU SEQRES 15 B 210 ASP GLN ASN PRO HIS LEU ALA GLN GLU LEU ARG PRO GLN SEQRES 16 B 210 ILE GLN GLU LEU LEU HIS SER GLU HIS LEU GLY PRO SER SEQRES 17 B 210 GLU LEU HET IDS C 1 17 HET SGN C 2 19 HET IDS C 3 16 HET SGN C 4 19 HET UAP C 5 15 HET IDS D 1 17 HET SGN D 2 19 HET IDS D 3 16 HET SGN D 4 19 HET IDS D 5 16 HET SGN D 6 19 HET ZN A 506 1 HETNAM IDS 2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID HETNAM SGN 2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-ALPHA-D-GLUCOPYRANOSE HETNAM UAP 4-DEOXY-2-O-SULFO-ALPHA-L-THREO-HEX-4-ENOPYRANURONIC HETNAM 2 UAP ACID HETNAM ZN ZINC ION HETSYN IDS O2-SULFO-GLUCURONIC ACID; 2-O-SULFO-ALPHA-L-IDURONIC HETSYN 2 IDS ACID; 2-O-SULFO-L-IDURONIC ACID; 2-O-SULFO-IDURONIC HETSYN 3 IDS ACID HETSYN SGN N,O6-DISULFO-GLUCOSAMINE; 6-O-SULFO-N-SULFO-ALPHA-D- HETSYN 2 SGN GLUCOSAMINE; 2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-ALPHA-D- HETSYN 3 SGN GLUCOSE; 2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-D-GLUCOSE; HETSYN 4 SGN 2-DEOXY-6-O-SULFO-2-(SULFOAMINO)-GLUCOSE HETSYN UAP 4-DEOXY-2-O-SULFO-ALPHA-L-THREO-HEX-4-ENURONIC ACID; 4- HETSYN 2 UAP DEOXY-2-O-SULFO-L-THREO-HEX-4-ENURONIC ACID; 4-DEOXY- HETSYN 3 UAP 2-O-SULFO-THREO-HEX-4-ENURONIC ACID FORMUL 3 IDS 5(C6 H10 O10 S) FORMUL 3 SGN 5(C6 H13 N O11 S2) FORMUL 3 UAP C6 H8 O9 S FORMUL 5 ZN ZN 2+ FORMUL 6 HOH *68(H2 O) HELIX 1 1 ASP A 292 GLY A 299 1 8 HELIX 2 2 SER A 305 SER A 339 1 35 HELIX 3 3 PRO A 343 GLN A 400 1 58 HELIX 4 4 GLN A 405 ASP A 438 1 34 HELIX 5 5 ASP A 438 GLN A 444 1 7 HELIX 6 6 MET A 445 GLY A 465 1 21 HELIX 7 7 LEU A 466 GLN A 469 5 4 HELIX 8 8 ASN A 470 SER A 487 1 18 HELIX 9 9 GLY B 293 GLY B 299 1 7 HELIX 10 10 SER B 305 SER B 339 1 35 HELIX 11 11 PRO B 343 ALA B 401 1 59 HELIX 12 12 GLN B 405 ASP B 438 1 34 HELIX 13 13 ASP B 438 GLN B 469 1 32 HELIX 14 14 ASN B 470 HIS B 486 1 17 LINK O4 IDS C 1 C1 SGN C 2 1555 1555 1.45 LINK O4 SGN C 2 C1 IDS C 3 1555 1555 1.43 LINK O4 IDS C 3 C1 SGN C 4 1555 1555 1.45 LINK O4 SGN C 4 C1 UAP C 5 1555 1555 1.45 LINK O4 IDS D 1 C1 SGN D 2 1555 1555 1.45 LINK O4 SGN D 2 C1 IDS D 3 1555 1555 1.45 LINK O4 IDS D 3 C1 SGN D 4 1555 1555 1.45 LINK O4 SGN D 4 C1 IDS D 5 1555 1555 1.44 LINK O4 IDS D 5 C1 SGN D 6 1555 1555 1.45 LINK NE2 HIS A 486 ZN ZN A 506 1555 1555 1.97 CISPEP 1 ASP A 402 PRO A 403 0 0.49 CISPEP 2 ASP B 402 PRO B 403 0 -1.41 CRYST1 91.969 91.969 208.481 90.00 90.00 120.00 P 31 2 1 12 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 0.010873 0.006278 0.000000 0.00000 SCALE2 0.000000 0.012555 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004797 0.00000