PDB Short entry for 5X1A HEADER PROTEIN BINDING 25-JAN-17 5X1A TITLE CRYSTAL STRUCTURE OF HUMAN CRMP-2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROPYRIMIDINASE-RELATED PROTEIN 2; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 1-525; COMPND 5 SYNONYM: DRP-2,COLLAPSIN RESPONSE MEDIATOR PROTEIN 2,CRMP-2,N2A3,UNC- COMPND 6 33-LIKE PHOSPHOPROTEIN 2,ULIP-2; COMPND 7 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: DPYSL2, CRMP2, ULIP2; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS DEVELOPMENTAL PROTEIN, PHOSPHOPROTEIN, MICROTUBULE ASSOCIATED KEYWDS 2 PROTEINS, NEUROGENESIS, DIHYDROPYRIMIDASE-RELATED PROTEIN, COLLAPSIN KEYWDS 3 RESPONSE MEDIATOR PROTEIN, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR R.NITTA,Y.TOMABECHI,M.AOKI,M.SHIROUZU REVDAT 3 20-MAR-24 5X1A 1 REMARK REVDAT 2 27-SEP-17 5X1A 1 REMARK REVDAT 1 20-SEP-17 5X1A 0 JRNL AUTH S.NIWA,F.NAKAMURA,Y.TOMABECHI,M.AOKI,H.SHIGEMATSU, JRNL AUTH 2 T.MATSUMOTO,A.YAMAGATA,S.FUKAI,N.HIROKAWA,Y.GOSHIMA, JRNL AUTH 3 M.SHIROUZU,R.NITTA JRNL TITL STRUCTURAL BASIS FOR CRMP2-INDUCED AXONAL MICROTUBULE JRNL TITL 2 FORMATION JRNL REF SCI REP V. 7 10681 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 28878401 JRNL DOI 10.1038/S41598-017-11031-4 REMARK 2 REMARK 2 RESOLUTION. 1.82 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.82 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.34 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 57874 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.188 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.070 REMARK 3 FREE R VALUE TEST SET COUNT : 2934 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 37.3522 - 5.0207 0.99 2812 135 0.1594 0.1417 REMARK 3 2 5.0207 - 3.9865 1.00 2686 157 0.1346 0.1555 REMARK 3 3 3.9865 - 3.4830 1.00 2649 158 0.1598 0.1894 REMARK 3 4 3.4830 - 3.1648 1.00 2633 136 0.1882 0.2296 REMARK 3 5 3.1648 - 2.9380 1.00 2632 150 0.1945 0.2307 REMARK 3 6 2.9380 - 2.7649 1.00 2657 119 0.1955 0.2569 REMARK 3 7 2.7649 - 2.6264 1.00 2625 142 0.1866 0.2359 REMARK 3 8 2.6264 - 2.5121 1.00 2621 134 0.1953 0.2194 REMARK 3 9 2.5121 - 2.4154 1.00 2604 144 0.1979 0.2250 REMARK 3 10 2.4154 - 2.3321 1.00 2594 133 0.2084 0.2701 REMARK 3 11 2.3321 - 2.2592 1.00 2612 140 0.2125 0.2311 REMARK 3 12 2.2592 - 2.1946 1.00 2603 121 0.2184 0.2290 REMARK 3 13 2.1946 - 2.1368 1.00 2611 145 0.2247 0.2930 REMARK 3 14 2.1368 - 2.0847 1.00 2575 168 0.2234 0.2577 REMARK 3 15 2.0847 - 2.0373 1.00 2595 122 0.2309 0.3060 REMARK 3 16 2.0373 - 1.9940 1.00 2576 136 0.2405 0.2631 REMARK 3 17 1.9940 - 1.9541 1.00 2578 156 0.2529 0.2640 REMARK 3 18 1.9541 - 1.9172 1.00 2606 121 0.2414 0.2991 REMARK 3 19 1.9172 - 1.8830 1.00 2587 152 0.2539 0.2581 REMARK 3 20 1.8830 - 1.8511 1.00 2576 129 0.2633 0.3050 REMARK 3 21 1.8511 - 1.8212 0.97 2508 136 0.3029 0.3713 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) : 0.210 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 23.240 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 : 0.008 3871 REMARK 3 ANGLE : 1.133 5254 REMARK 3 CHIRALITY : 0.045 592 REMARK 3 PLANARITY : 0.006 686 REMARK 3 DIHEDRAL : 14.709 1418 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 5X1A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-FEB-17. REMARK 100 THE DEPOSITION ID IS D_1300002772. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57910 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.820 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 14.50 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.79 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.78 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 8000, TRIS PH 8.5, DTT, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 41 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 3555 -Y,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X,Z+3/4 REMARK 290 5555 -X+1/2,Y,-Z+3/4 REMARK 290 6555 X,-Y+1/2,-Z+1/4 REMARK 290 7555 Y+1/2,X+1/2,-Z+1/2 REMARK 290 8555 -Y,-X,-Z REMARK 290 9555 X+1/2,Y+1/2,Z+1/2 REMARK 290 10555 -X,-Y,Z REMARK 290 11555 -Y+1/2,X,Z+3/4 REMARK 290 12555 Y,-X+1/2,Z+1/4 REMARK 290 13555 -X,Y+1/2,-Z+1/4 REMARK 290 14555 X+1/2,-Y,-Z+3/4 REMARK 290 15555 Y,X,-Z REMARK 290 16555 -Y+1/2,-X+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 57.06050 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 57.06050 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 98.06300 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 57.06050 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 49.03150 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 57.06050 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 147.09450 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 57.06050 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 147.09450 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 57.06050 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 49.03150 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 57.06050 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 57.06050 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 98.06300 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 1.000000 0.000000 0.000000 57.06050 REMARK 290 SMTRY2 9 0.000000 1.000000 0.000000 57.06050 REMARK 290 SMTRY3 9 0.000000 0.000000 1.000000 98.06300 REMARK 290 SMTRY1 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 -1.000000 0.000000 57.06050 REMARK 290 SMTRY2 11 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 1.000000 147.09450 REMARK 290 SMTRY1 12 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 -1.000000 0.000000 0.000000 57.06050 REMARK 290 SMTRY3 12 0.000000 0.000000 1.000000 49.03150 REMARK 290 SMTRY1 13 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 13 0.000000 1.000000 0.000000 57.06050 REMARK 290 SMTRY3 13 0.000000 0.000000 -1.000000 49.03150 REMARK 290 SMTRY1 14 1.000000 0.000000 0.000000 57.06050 REMARK 290 SMTRY2 14 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 14 0.000000 0.000000 -1.000000 147.09450 REMARK 290 SMTRY1 15 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 15 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 15 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 16 0.000000 -1.000000 0.000000 57.06050 REMARK 290 SMTRY2 16 -1.000000 0.000000 0.000000 57.06050 REMARK 290 SMTRY3 16 0.000000 0.000000 -1.000000 98.06300 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 0.000000 -1.000000 0.000000 114.12100 REMARK 350 BIOMT2 2 -1.000000 0.000000 0.000000 114.12100 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 114.12100 REMARK 350 BIOMT2 3 0.000000 -1.000000 0.000000 114.12100 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 4 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 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 833 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 842 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 871 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 900 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 923 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 992 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 994 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 MET A 1 REMARK 465 SER A 2 REMARK 465 TYR A 3 REMARK 465 GLN A 4 REMARK 465 GLY A 5 REMARK 465 LYS A 6 REMARK 465 LYS A 7 REMARK 465 ASN A 8 REMARK 465 ILE A 9 REMARK 465 PRO A 10 REMARK 465 ARG A 11 REMARK 465 ILE A 12 REMARK 465 THR A 13 REMARK 465 SER A 507 REMARK 465 VAL A 508 REMARK 465 THR A 509 REMARK 465 PRO A 510 REMARK 465 LYS A 511 REMARK 465 THR A 512 REMARK 465 VAL A 513 REMARK 465 THR A 514 REMARK 465 PRO A 515 REMARK 465 ALA A 516 REMARK 465 SER A 517 REMARK 465 SER A 518 REMARK 465 ALA A 519 REMARK 465 LYS A 520 REMARK 465 THR A 521 REMARK 465 SER A 522 REMARK 465 PRO A 523 REMARK 465 ALA A 524 REMARK 465 LYS A 525 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 NZ LYS A 483 O HOH A 601 1.82 REMARK 500 O HOH A 771 O HOH A 964 1.91 REMARK 500 O HOH A 932 O HOH A 964 1.93 REMARK 500 O HOH A 735 O HOH A 830 1.97 REMARK 500 O HOH A 754 O HOH A 890 2.04 REMARK 500 O HOH A 835 O HOH A 914 2.05 REMARK 500 NE2 GLN A 29 O HOH A 602 2.06 REMARK 500 O LYS A 345 O HOH A 603 2.09 REMARK 500 O HOH A 967 O HOH A 1000 2.11 REMARK 500 O HOH A 605 O HOH A 634 2.12 REMARK 500 O HOH A 865 O HOH A 916 2.12 REMARK 500 O HOH A 811 O HOH A 899 2.16 REMARK 500 O HOH A 880 O HOH A 935 2.16 REMARK 500 OE2 GLU A 150 O HOH A 604 2.18 REMARK 500 O HOH A 724 O HOH A 796 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 O HOH A 899 O HOH A 899 15555 2.15 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 15 -162.94 32.11 REMARK 500 ASN A 48 108.18 -5.41 REMARK 500 GLN A 77 45.77 32.05 REMARK 500 ALA A 169 -161.94 -121.66 REMARK 500 ARG A 173 -71.70 -133.94 REMARK 500 CYS A 334 84.99 -152.78 REMARK 500 SER A 385 -48.27 -146.60 REMARK 500 ALA A 489 -116.01 -11.48 REMARK 500 GLU A 490 -78.76 -151.12 REMARK 500 LEU A 491 91.31 49.92 REMARK 500 LEU A 498 -34.73 102.09 REMARK 500 TYR A 499 103.32 69.59 REMARK 500 GLU A 505 -84.34 -55.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 47 ASN A 48 -146.09 REMARK 500 ALA A 489 GLU A 490 -132.31 REMARK 500 GLU A 490 LEU A 491 -147.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5X1C RELATED DB: PDB REMARK 900 RELATED ID: 5X1D RELATED DB: PDB DBREF 5X1A A 1 525 UNP Q16555 DPYL2_HUMAN 1 525 SEQRES 1 A 525 MET SER TYR GLN GLY LYS LYS ASN ILE PRO ARG ILE THR SEQRES 2 A 525 SER ASP ARG LEU LEU ILE LYS GLY GLY LYS ILE VAL ASN SEQRES 3 A 525 ASP ASP GLN SER PHE TYR ALA ASP ILE TYR MET GLU ASP SEQRES 4 A 525 GLY LEU ILE LYS GLN ILE GLY GLU ASN LEU ILE VAL PRO SEQRES 5 A 525 GLY GLY VAL LYS THR ILE GLU ALA HIS SER ARG MET VAL SEQRES 6 A 525 ILE PRO GLY GLY ILE ASP VAL HIS THR ARG PHE GLN MET SEQRES 7 A 525 PRO ASP GLN GLY MET THR SER ALA ASP ASP PHE PHE GLN SEQRES 8 A 525 GLY THR LYS ALA ALA LEU ALA GLY GLY THR THR MET ILE SEQRES 9 A 525 ILE ASP HIS VAL VAL PRO GLU PRO GLY THR SER LEU LEU SEQRES 10 A 525 ALA ALA PHE ASP GLN TRP ARG GLU TRP ALA ASP SER LYS SEQRES 11 A 525 SER CYS CYS ASP TYR SER LEU HIS VAL ASP ILE SER GLU SEQRES 12 A 525 TRP HIS LYS GLY ILE GLN GLU GLU MET GLU ALA LEU VAL SEQRES 13 A 525 LYS ASP HIS GLY VAL ASN SER PHE LEU VAL TYR MET ALA SEQRES 14 A 525 PHE LYS ASP ARG PHE GLN LEU THR ASP CYS GLN ILE TYR SEQRES 15 A 525 GLU VAL LEU SER VAL ILE ARG ASP ILE GLY ALA ILE ALA SEQRES 16 A 525 GLN VAL HIS ALA GLU ASN GLY ASP ILE ILE ALA GLU GLU SEQRES 17 A 525 GLN GLN ARG ILE LEU ASP LEU GLY ILE THR GLY PRO GLU SEQRES 18 A 525 GLY HIS VAL LEU SER ARG PRO GLU GLU VAL GLU ALA GLU SEQRES 19 A 525 ALA VAL ASN ARG ALA ILE THR ILE ALA ASN GLN THR ASN SEQRES 20 A 525 CYS PRO LEU TYR ILE THR LYS VAL MET SER LYS SER SER SEQRES 21 A 525 ALA GLU VAL ILE ALA GLN ALA ARG LYS LYS GLY THR VAL SEQRES 22 A 525 VAL TYR GLY GLU PRO ILE THR ALA SER LEU GLY THR ASP SEQRES 23 A 525 GLY SER HIS TYR TRP SER LYS ASN TRP ALA LYS ALA ALA SEQRES 24 A 525 ALA PHE VAL THR SER PRO PRO LEU SER PRO ASP PRO THR SEQRES 25 A 525 THR PRO ASP PHE LEU ASN SER LEU LEU SER CYS GLY ASP SEQRES 26 A 525 LEU GLN VAL THR GLY SER ALA HIS CYS THR PHE ASN THR SEQRES 27 A 525 ALA GLN LYS ALA VAL GLY LYS ASP ASN PHE THR LEU ILE SEQRES 28 A 525 PRO GLU GLY THR ASN GLY THR GLU GLU ARG MET SER VAL SEQRES 29 A 525 ILE TRP ASP LYS ALA VAL VAL THR GLY LYS MET ASP GLU SEQRES 30 A 525 ASN GLN PHE VAL ALA VAL THR SER THR ASN ALA ALA LYS SEQRES 31 A 525 VAL PHE ASN LEU TYR PRO ARG LYS GLY ARG ILE ALA VAL SEQRES 32 A 525 GLY SER ASP ALA ASP LEU VAL ILE TRP ASP PRO ASP SER SEQRES 33 A 525 VAL LYS THR ILE SER ALA LYS THR HIS ASN SER SER LEU SEQRES 34 A 525 GLU TYR ASN ILE PHE GLU GLY MET GLU CYS ARG GLY SER SEQRES 35 A 525 PRO LEU VAL VAL ILE SER GLN GLY LYS ILE VAL LEU GLU SEQRES 36 A 525 ASP GLY THR LEU HIS VAL THR GLU GLY SER GLY ARG TYR SEQRES 37 A 525 ILE PRO ARG LYS PRO PHE PRO ASP PHE VAL TYR LYS ARG SEQRES 38 A 525 ILE LYS ALA ARG SER ARG LEU ALA GLU LEU ARG GLY VAL SEQRES 39 A 525 PRO ARG GLY LEU TYR ASP GLY PRO VAL CYS GLU VAL SER SEQRES 40 A 525 VAL THR PRO LYS THR VAL THR PRO ALA SER SER ALA LYS SEQRES 41 A 525 THR SER PRO ALA LYS FORMUL 2 HOH *400(H2 O) HELIX 1 AA1 ASP A 88 GLY A 99 1 12 HELIX 2 AA2 SER A 115 SER A 131 1 17 HELIX 3 AA3 GLY A 147 HIS A 159 1 13 HELIX 4 AA4 THR A 177 GLY A 192 1 16 HELIX 5 AA5 ASN A 201 LEU A 215 1 15 HELIX 6 AA6 PRO A 220 SER A 226 1 7 HELIX 7 AA7 PRO A 228 ASN A 247 1 20 HELIX 8 AA8 SER A 257 GLY A 271 1 15 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 ALA A 300 1 7 HELIX 12 AB3 THR A 312 CYS A 323 1 12 HELIX 13 AB4 ASN 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 PHE A 392 1 8 HELIX 19 AC1 PRO A 475 ARG A 487 1 13 SHEET 1 AA1 4 LEU A 41 GLY A 46 0 SHEET 2 AA1 4 SER A 30 GLU A 38 -1 N ASP A 34 O GLY A 46 SHEET 3 AA1 4 LEU A 17 VAL A 25 -1 N LEU A 17 O MET A 37 SHEET 4 AA1 4 LYS A 56 GLU A 59 1 O ILE A 58 N LYS A 20 SHEET 1 AA2 8 LEU A 41 GLY A 46 0 SHEET 2 AA2 8 SER A 30 GLU A 38 -1 N ASP A 34 O GLY A 46 SHEET 3 AA2 8 LEU A 17 VAL A 25 -1 N LEU A 17 O MET A 37 SHEET 4 AA2 8 MET A 64 PRO A 67 1 O VAL A 65 N LYS A 23 SHEET 5 AA2 8 LEU A 409 THR A 419 -1 O VAL A 410 N ILE A 66 SHEET 6 AA2 8 GLU A 438 SER A 448 -1 O LEU A 444 N ILE A 411 SHEET 7 AA2 8 LYS A 451 GLU A 455 -1 O VAL A 453 N VAL A 446 SHEET 8 AA2 8 THR A 458 LEU A 459 -1 O THR 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 ASP A 140 1 O HIS A 138 N ASP A 106 SHEET 4 AA3 7 SER A 163 TYR A 167 1 O SER A 163 N VAL A 139 SHEET 5 AA3 7 ILE 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 TYR A 275 N ILE A 252 SHEET 1 AA4 2 PRO A 79 ASP A 80 0 SHEET 2 AA4 2 MET A 83 THR A 84 -1 O MET A 83 N ASP A 80 CISPEP 1 SER A 304 PRO A 305 0 -6.77 CISPEP 2 TYR A 395 PRO A 396 0 5.25 CRYST1 114.121 114.121 196.126 90.00 90.00 90.00 I 41 2 2 16 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 0.008763 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008763 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005099 0.00000