HEADER HYDROLASE 31-MAR-17 5NKS TITLE HUMAN DIHYDROPYRIMIDINASE-RELATED PROTEIN 4 (DPYSL4, CRMP3, ULIP-4) COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROPYRIMIDINASE-RELATED PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DRP-4,COLLAPSIN RESPONSE MEDIATOR PROTEIN 3,CRMP-3,UNC33- COMPND 5 LIKE PHOSPHOPROTEIN 4,ULIP-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: DPYSL4, CRMP3, ULIP4; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108 KEYWDS HYDROLASE, CYTOSKELETON, NEUROPLASTICITY, TETRAMERISATION EXPDTA X-RAY DIFFRACTION AUTHOR S.MATHEA,J.M.ELKINS,C.STRAIN-DAMERELL,E.SALAH,O.BORKOWSKA,R.CHALK, AUTHOR 2 N.BURGESS-BROWN,D.M.PINKAS,F.VON DELFT,T.KROJER,C.H.ARROWSMITH, AUTHOR 3 A.M.EDWARDS,C.BOUNTRA,S.KNAPP REVDAT 2 17-JAN-24 5NKS 1 REMARK REVDAT 1 01-NOV-17 5NKS 0 JRNL AUTH S.MATHEA,S.KNAPP JRNL TITL HUMAN DIHYDROPYRIMIDINASE-RELATED PROTEIN 4 (DPYSL4, CRMP3, JRNL TITL 2 ULIP-4) JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 77.16 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 3 NUMBER OF REFLECTIONS : 42105 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : 0.157 REMARK 3 R VALUE (WORKING SET) : 0.155 REMARK 3 FREE R VALUE : 0.200 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2200 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3003 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.2810 REMARK 3 BIN FREE R VALUE SET COUNT : 150 REMARK 3 BIN FREE R VALUE : 0.3240 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3698 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 314 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.73 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.69000 REMARK 3 B22 (A**2) : 2.04000 REMARK 3 B33 (A**2) : -0.34000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.113 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.115 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.096 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.332 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3826 ; 0.018 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3613 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5206 ; 1.831 ; 1.945 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8309 ; 1.055 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 499 ; 5.992 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 162 ;34.116 ;24.321 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 617 ;13.163 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;16.301 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 592 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4401 ; 0.009 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 856 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1981 ; 1.904 ; 2.173 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1980 ; 1.897 ; 2.171 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2482 ; 2.685 ; 3.247 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2483 ; 2.685 ; 3.249 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1844 ; 2.922 ; 2.497 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1845 ; 2.921 ; 2.499 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2724 ; 4.330 ; 3.622 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4491 ; 5.875 ;18.403 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4378 ; 5.762 ;18.111 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5NKS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-APR-17. REMARK 100 THE DEPOSITION ID IS D_1200004271. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9797 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 44328 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 27.850 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.84 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.6 REMARK 200 DATA REDUNDANCY IN SHELL : 2.90 REMARK 200 R MERGE FOR SHELL (I) : 0.65100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4BKN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.82 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.95 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS-PROPANE 0.2 M SODIUM REMARK 280 FLUORIDE 10% ETHYLENE GLYCOL 20% PEG3350, PH 6.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z REMARK 290 3555 -X,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 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+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 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 40.23500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 51.32500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 58.49500 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 40.23500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 51.32500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 58.49500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 40.23500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 51.32500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 58.49500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 40.23500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 51.32500 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 58.49500 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 -116.99000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 -116.99000 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 865 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 877 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 0 REMARK 465 MET A 1 REMARK 465 SER A 2 REMARK 465 PHE A 3 REMARK 465 GLN A 4 REMARK 465 GLY A 5 REMARK 465 ARG A 496 REMARK 465 GLY A 497 REMARK 465 LEU A 498 REMARK 465 TYR A 499 REMARK 465 ASP A 500 REMARK 465 GLY A 501 REMARK 465 PRO A 502 REMARK 465 VAL A 503 REMARK 465 HIS A 504 REMARK 465 GLU A 505 REMARK 465 VAL A 506 REMARK 465 MET A 507 REMARK 465 VAL A 508 REMARK 465 PRO A 509 REMARK 465 ALA A 510 REMARK 465 LYS A 511 REMARK 465 PRO A 512 REMARK 465 GLY A 513 REMARK 465 SER A 514 REMARK 465 GLY A 515 REMARK 465 ALA A 516 REMARK 465 PRO A 517 REMARK 465 ALA A 518 REMARK 465 ARG A 519 REMARK 465 ALA A 520 REMARK 465 SER A 521 REMARK 465 CYS A 522 REMARK 465 PRO A 523 REMARK 465 GLY A 524 REMARK 465 LYS A 525 REMARK 465 ILE A 526 REMARK 465 SER A 527 REMARK 465 VAL A 528 REMARK 465 PRO A 529 REMARK 465 PRO A 530 REMARK 465 VAL A 531 REMARK 465 ARG A 532 REMARK 465 ASN A 533 REMARK 465 LEU A 534 REMARK 465 HIS A 535 REMARK 465 GLN A 536 REMARK 465 SER A 537 REMARK 465 GLY A 538 REMARK 465 PHE A 539 REMARK 465 SER A 540 REMARK 465 LEU A 541 REMARK 465 SER A 542 REMARK 465 GLY A 543 REMARK 465 SER A 544 REMARK 465 GLN A 545 REMARK 465 ALA A 546 REMARK 465 ASP A 547 REMARK 465 ASP A 548 REMARK 465 HIS A 549 REMARK 465 ILE A 550 REMARK 465 ALA A 551 REMARK 465 ARG A 552 REMARK 465 ARG A 553 REMARK 465 THR A 554 REMARK 465 ALA A 555 REMARK 465 GLN A 556 REMARK 465 LYS A 557 REMARK 465 ILE A 558 REMARK 465 MET A 559 REMARK 465 ALA A 560 REMARK 465 PRO A 561 REMARK 465 PRO A 562 REMARK 465 GLY A 563 REMARK 465 GLY A 564 REMARK 465 ARG A 565 REMARK 465 SER A 566 REMARK 465 ASN A 567 REMARK 465 ILE A 568 REMARK 465 THR A 569 REMARK 465 SER A 570 REMARK 465 LEU A 571 REMARK 465 SER A 572 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 7 CD CE NZ REMARK 470 ILE A 12 CG1 CG2 CD1 REMARK 470 ARG A 16 CZ NH1 NH2 REMARK 470 LYS A 43 CE NZ REMARK 470 GLU A 47 CG CD OE1 OE2 REMARK 470 ARG A 143 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 146 CG CD OE1 OE2 REMARK 470 ASP A 172 CG OD1 OD2 REMARK 470 ARG A 211 NE CZ NH1 NH2 REMARK 470 LYS A 244 CE NZ REMARK 470 LYS A 293 CG CD CE NZ REMARK 470 LYS A 345 CD CE NZ REMARK 470 LYS A 418 CG CD CE NZ REMARK 470 LYS A 458 CG CD CE NZ REMARK 470 LYS A 472 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NH2 ARG A 269 NH2 ARG A 269 2555 1.93 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 GLU A 234 CD GLU A 234 OE1 0.067 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASP A 34 CB - CG - OD1 ANGL. DEV. = 5.6 DEGREES REMARK 500 ARG A 189 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 269 CG - CD - NE ANGL. DEV. = -16.4 DEGREES REMARK 500 ARG A 269 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 361 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG A 400 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ARG A 173 -68.16 -142.88 REMARK 500 CYS A 334 88.59 -162.31 REMARK 500 ASN A 347 106.41 -162.72 REMARK 500 SER A 385 -48.44 -146.54 REMARK 500 ASN A 393 45.43 78.70 REMARK 500 ASN A 426 41.91 -99.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 913 DISTANCE = 6.09 ANGSTROMS REMARK 525 HOH A 914 DISTANCE = 6.67 ANGSTROMS DBREF 5NKS A 1 572 UNP O14531 DPYL4_HUMAN 1 572 SEQADV 5NKS SER A 0 UNP O14531 EXPRESSION TAG SEQRES 1 A 573 SER MET SER PHE GLN GLY LYS LYS SER ILE PRO ARG ILE SEQRES 2 A 573 THR SER ASP ARG LEU LEU ILE ARG GLY GLY ARG ILE VAL SEQRES 3 A 573 ASN ASP ASP GLN SER PHE TYR ALA ASP VAL HIS VAL GLU SEQRES 4 A 573 ASP GLY LEU ILE LYS GLN ILE GLY GLU ASN LEU ILE VAL SEQRES 5 A 573 PRO GLY GLY ILE LYS THR ILE ASP ALA HIS GLY LEU MET SEQRES 6 A 573 VAL LEU PRO GLY GLY VAL ASP VAL HIS THR ARG LEU GLN SEQRES 7 A 573 MET PRO VAL LEU GLY MET THR PRO ALA ASP ASP PHE CYS SEQRES 8 A 573 GLN GLY THR LYS ALA ALA LEU ALA GLY GLY THR THR MET SEQRES 9 A 573 ILE LEU ASP HIS VAL PHE PRO ASP THR GLY VAL SER LEU SEQRES 10 A 573 LEU ALA ALA TYR GLU GLN TRP ARG GLU ARG ALA ASP SER SEQRES 11 A 573 ALA ALA CYS CYS ASP TYR SER LEU HIS VAL ASP ILE THR SEQRES 12 A 573 ARG TRP HIS GLU SER ILE LYS GLU GLU LEU GLU ALA LEU SEQRES 13 A 573 VAL LYS GLU LYS GLY VAL ASN SER PHE LEU VAL PHE MET SEQRES 14 A 573 ALA TYR LYS ASP ARG CYS GLN CYS SER ASP SER GLN MET SEQRES 15 A 573 TYR GLU ILE PHE SER ILE ILE ARG ASP LEU GLY ALA LEU SEQRES 16 A 573 ALA GLN VAL HIS ALA GLU ASN GLY ASP ILE VAL GLU GLU SEQRES 17 A 573 GLU GLN LYS ARG LEU LEU GLU LEU GLY ILE THR GLY PRO SEQRES 18 A 573 GLU GLY HIS VAL LEU SER HIS PRO GLU GLU VAL GLU ALA SEQRES 19 A 573 GLU ALA VAL TYR ARG ALA VAL THR ILE ALA LYS GLN ALA SEQRES 20 A 573 ASN CYS PRO LEU TYR VAL THR LYS VAL MET SER LYS GLY SEQRES 21 A 573 ALA ALA ASP ALA ILE ALA GLN ALA LYS ARG ARG GLY VAL SEQRES 22 A 573 VAL VAL PHE GLY GLU PRO ILE THR ALA SER LEU GLY THR SEQRES 23 A 573 ASP GLY SER HIS TYR TRP SER LYS ASN TRP ALA LYS ALA SEQRES 24 A 573 ALA ALA PHE VAL THR SER PRO PRO VAL ASN PRO ASP PRO SEQRES 25 A 573 THR THR ALA ASP HIS LEU THR CYS LEU LEU SER SER GLY SEQRES 26 A 573 ASP LEU GLN VAL THR GLY SER ALA HIS CYS THR PHE THR SEQRES 27 A 573 THR ALA GLN LYS ALA VAL GLY LYS ASP ASN PHE ALA LEU SEQRES 28 A 573 ILE PRO GLU GLY THR ASN GLY ILE GLU GLU ARG MET SER SEQRES 29 A 573 MET VAL TRP GLU LYS CYS VAL ALA SER GLY LYS MET ASP SEQRES 30 A 573 GLU ASN GLU PHE VAL ALA VAL THR SER THR ASN ALA ALA SEQRES 31 A 573 LYS ILE PHE ASN PHE TYR PRO ARG LYS GLY ARG VAL ALA SEQRES 32 A 573 VAL GLY SER ASP ALA ASP LEU VAL ILE TRP ASN PRO LYS SEQRES 33 A 573 ALA THR LYS ILE ILE SER ALA LYS THR HIS ASN LEU ASN SEQRES 34 A 573 VAL GLU TYR ASN ILE PHE GLU GLY VAL GLU CYS ARG GLY SEQRES 35 A 573 ALA PRO ALA VAL VAL ILE SER GLN GLY ARG VAL ALA LEU SEQRES 36 A 573 GLU ASP GLY LYS MET PHE VAL THR PRO GLY ALA GLY ARG SEQRES 37 A 573 PHE VAL PRO ARG LYS THR PHE PRO ASP PHE VAL TYR LYS SEQRES 38 A 573 ARG ILE LYS ALA ARG ASN ARG LEU ALA GLU ILE HIS GLY SEQRES 39 A 573 VAL PRO ARG GLY LEU TYR ASP GLY PRO VAL HIS GLU VAL SEQRES 40 A 573 MET VAL PRO ALA LYS PRO GLY SER GLY ALA PRO ALA ARG SEQRES 41 A 573 ALA SER CYS PRO GLY LYS ILE SER VAL PRO PRO VAL ARG SEQRES 42 A 573 ASN LEU HIS GLN SER GLY PHE SER LEU SER GLY SER GLN SEQRES 43 A 573 ALA ASP ASP HIS ILE ALA ARG ARG THR ALA GLN LYS ILE SEQRES 44 A 573 MET ALA PRO PRO GLY GLY ARG SER ASN ILE THR SER LEU SEQRES 45 A 573 SER FORMUL 2 HOH *314(H2 O) HELIX 1 AA1 ASP A 88 GLY A 99 1 12 HELIX 2 AA2 SER A 115 ALA A 131 1 17 HELIX 3 AA3 SER A 147 LYS A 159 1 13 HELIX 4 AA4 SER A 177 LEU A 191 1 15 HELIX 5 AA5 ASN A 201 LEU A 215 1 15 HELIX 6 AA6 GLY A 219 SER A 226 1 8 HELIX 7 AA7 PRO A 228 ASN A 247 1 20 HELIX 8 AA8 SER A 257 ARG A 270 1 14 HELIX 9 AA9 ILE A 279 THR A 285 1 7 HELIX 10 AB1 ASP A 286 SER A 292 5 7 HELIX 11 AB2 ASN A 294 PHE A 301 1 8 HELIX 12 AB3 THR A 312 SER A 323 1 12 HELIX 13 AB4 THR A 337 ALA A 342 1 6 HELIX 14 AB5 VAL A 343 LYS A 345 5 3 HELIX 15 AB6 ASN A 347 ILE A 351 5 5 HELIX 16 AB7 GLU A 360 VAL A 370 1 11 HELIX 17 AB8 ASP A 376 SER A 385 1 10 HELIX 18 AB9 SER A 385 ASN A 393 1 9 HELIX 19 AC1 PRO A 475 HIS A 492 1 18 SHEET 1 AA1 4 LEU A 41 GLY A 46 0 SHEET 2 AA1 4 ASP A 34 GLU A 38 -1 N HIS A 36 O LYS A 43 SHEET 3 AA1 4 LEU A 17 ARG A 20 -1 N ILE A 19 O VAL A 35 SHEET 4 AA1 4 THR A 57 ASP A 59 1 O ILE A 58 N ARG A 20 SHEET 1 AA2 7 SER A 30 TYR A 32 0 SHEET 2 AA2 7 ARG A 23 VAL A 25 -1 N ILE A 24 O PHE A 31 SHEET 3 AA2 7 MET A 64 PRO A 67 1 O VAL A 65 N VAL A 25 SHEET 4 AA2 7 LEU A 409 ILE A 419 -1 O VAL A 410 N LEU A 66 SHEET 5 AA2 7 GLU A 438 SER A 448 -1 O ALA A 444 N ILE A 411 SHEET 6 AA2 7 ARG A 451 GLU A 455 -1 O ALA A 453 N VAL A 446 SHEET 7 AA2 7 LYS A 458 MET A 459 -1 O LYS A 458 N GLU A 455 SHEET 1 AA3 7 GLY A 69 THR A 74 0 SHEET 2 AA3 7 THR A 101 VAL A 108 1 O MET A 103 N ASP A 71 SHEET 3 AA3 7 ASP A 134 ILE A 141 1 O ASP A 140 N VAL A 108 SHEET 4 AA3 7 SER A 163 PHE A 167 1 O LEU A 165 N ILE A 141 SHEET 5 AA3 7 LEU A 194 HIS A 198 1 O GLN A 196 N PHE A 164 SHEET 6 AA3 7 LEU A 250 VAL A 255 1 O TYR A 251 N ALA A 195 SHEET 7 AA3 7 VAL A 274 PRO A 278 1 O PHE A 275 N VAL A 252 CISPEP 1 SER A 304 PRO A 305 0 -5.96 CISPEP 2 TYR A 395 PRO A 396 0 5.21 CRYST1 80.470 102.650 116.990 90.00 90.00 90.00 I 2 2 2 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 0.012427 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009742 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008548 0.00000