HEADER PROTEIN BINDING 25-JAN-17 5X1C TITLE CRYSTAL STRUCTURE OF HUMAN CRMP-2 WITHOUT C-TERMINAL TAIL COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIHYDROPYRIMIDINASE-RELATED PROTEIN 2; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 13-490; 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 5X1C 1 REMARK REVDAT 2 27-SEP-17 5X1C 1 REMARK REVDAT 1 20-SEP-17 5X1C 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. 2.10 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.26 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 70576 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.179 REMARK 3 R VALUE (WORKING SET) : 0.177 REMARK 3 FREE R VALUE : 0.202 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 6.890 REMARK 3 FREE R VALUE TEST SET COUNT : 4864 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 43.2719 - 6.5213 1.00 2324 266 0.1574 0.1947 REMARK 3 2 6.5213 - 5.1789 1.00 2202 258 0.1636 0.1823 REMARK 3 3 5.1789 - 4.5251 1.00 2180 227 0.1313 0.1477 REMARK 3 4 4.5251 - 4.1117 1.00 2147 257 0.1203 0.1501 REMARK 3 5 4.1117 - 3.8172 1.00 2114 267 0.1341 0.1923 REMARK 3 6 3.8172 - 3.5922 1.00 2151 231 0.1511 0.1900 REMARK 3 7 3.5922 - 3.4124 1.00 2108 258 0.1650 0.1945 REMARK 3 8 3.4124 - 3.2639 1.00 2104 250 0.1701 0.2175 REMARK 3 9 3.2639 - 3.1383 1.00 2114 257 0.1881 0.2272 REMARK 3 10 3.1383 - 3.0301 1.00 2120 237 0.1984 0.2227 REMARK 3 11 3.0301 - 2.9353 1.00 2098 244 0.2003 0.2172 REMARK 3 12 2.9353 - 2.8514 1.00 2123 236 0.2056 0.2360 REMARK 3 13 2.8514 - 2.7764 1.00 2091 255 0.2040 0.2188 REMARK 3 14 2.7764 - 2.7087 1.00 2106 210 0.2113 0.2373 REMARK 3 15 2.7087 - 2.6471 1.00 2076 264 0.2018 0.2308 REMARK 3 16 2.6471 - 2.5908 1.00 2118 233 0.1994 0.2161 REMARK 3 17 2.5908 - 2.5389 1.00 2095 232 0.2006 0.2501 REMARK 3 18 2.5389 - 2.4910 1.00 2139 203 0.2049 0.2577 REMARK 3 19 2.4910 - 2.4466 1.00 2117 215 0.1929 0.2413 REMARK 3 20 2.4466 - 2.4051 1.00 2091 239 0.2006 0.2312 REMARK 3 21 2.4051 - 2.3663 1.00 2306 25 0.2039 0.2276 REMARK 3 22 2.3663 - 2.3299 1.00 2315 0 0.2124 0.0000 REMARK 3 23 2.3299 - 2.2956 1.00 2324 0 0.2105 0.0000 REMARK 3 24 2.2956 - 2.2633 1.00 2315 0 0.1993 0.0000 REMARK 3 25 2.2633 - 2.2327 1.00 2342 0 0.2052 0.0000 REMARK 3 26 2.2327 - 2.2037 1.00 2321 0 0.2112 0.0000 REMARK 3 27 2.2037 - 2.1762 1.00 2308 0 0.2207 0.0000 REMARK 3 28 2.1762 - 2.1500 1.00 2320 0 0.2244 0.0000 REMARK 3 29 2.1500 - 2.1250 1.00 2319 0 0.2222 0.0000 REMARK 3 30 2.1250 - 2.1011 0.96 2224 0 0.2266 0.0000 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) : 26.160 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 : 0.009 7549 REMARK 3 ANGLE : 1.199 10244 REMARK 3 CHIRALITY : 0.047 1157 REMARK 3 PLANARITY : 0.006 1334 REMARK 3 DIHEDRAL : 14.392 2757 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 5X1C 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_1300002775. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUL-14 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 : BL32XU 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 : 70654 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.100 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 (%) : 100.0 REMARK 200 DATA REDUNDANCY : 9.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 3.5000 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 FOR SHELL : NULL 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.11 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: AMMONIUM SULFATE, TRIS PH 7.0, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 42 21 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 -Y+1/2,X+1/2,Z+1/2 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/2 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 Y,X,-Z REMARK 290 8555 -Y,-X,-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 0.00000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 63.34350 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 63.34350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 74.10950 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 63.34350 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 63.34350 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 74.10950 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 63.34350 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 63.34350 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 74.10950 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 63.34350 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 63.34350 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 74.10950 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 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 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, 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 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -126.68700 REMARK 350 BIOMT3 2 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 623 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 719 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 852 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 599 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 683 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 825 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 VAL B 7 REMARK 465 LEU B 8 REMARK 465 PHE B 9 REMARK 465 GLN B 10 REMARK 465 GLY B 11 REMARK 465 PRO B 12 REMARK 465 THR B 13 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 GLU B 125 CD 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 600 O HOH A 790 1.80 REMARK 500 O HOH B 663 O HOH B 801 1.85 REMARK 500 O HOH A 741 O HOH A 814 1.94 REMARK 500 O HOH A 679 O HOH A 759 1.95 REMARK 500 OD1 ASP A 87 O HOH A 501 1.99 REMARK 500 O HOH B 626 O HOH B 802 2.00 REMARK 500 O HOH B 764 O HOH B 766 2.02 REMARK 500 O HOH A 800 O HOH B 761 2.04 REMARK 500 O HOH A 592 O HOH A 827 2.07 REMARK 500 O HOH A 680 O HOH A 796 2.09 REMARK 500 OD2 ASP A 315 O HOH A 502 2.14 REMARK 500 O HOH A 784 O HOH B 780 2.16 REMARK 500 O HOH B 749 O HOH B 816 2.16 REMARK 500 OG SER A 85 O HOH A 503 2.17 REMARK 500 O HOH A 764 O HOH A 857 2.17 REMARK 500 O HOH B 598 O HOH B 622 2.18 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 B 515 O HOH B 787 2545 2.09 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 LEU A 8 CA - CB - CG ANGL. DEV. = -17.7 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 LEU A 8 86.51 18.49 REMARK 500 SER A 14 36.24 -78.50 REMARK 500 ASP A 15 31.96 -91.48 REMARK 500 GLN A 77 8.39 121.58 REMARK 500 ASP A 88 -165.78 -73.33 REMARK 500 ASN A 162 22.13 -142.42 REMARK 500 PHE A 170 64.60 62.71 REMARK 500 ASP A 172 -18.44 79.72 REMARK 500 ASN A 347 108.59 -162.46 REMARK 500 SER A 385 -49.19 -144.00 REMARK 500 ASN A 426 54.09 -92.30 REMARK 500 GLN A 449 46.24 38.63 REMARK 500 ASP B 15 54.39 -145.05 REMARK 500 ARG B 16 105.37 53.07 REMARK 500 ASP B 172 -36.39 140.53 REMARK 500 ARG B 173 -55.65 -137.65 REMARK 500 CYS B 334 70.70 -157.42 REMARK 500 ASN B 347 107.13 -169.20 REMARK 500 SER B 385 -48.74 -144.93 REMARK 500 ASN B 393 39.04 72.01 REMARK 500 ASN B 426 30.48 -99.31 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 VAL A 7 LEU A 8 -117.43 REMARK 500 ASP B 172 ARG B 173 -146.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5X1A RELATED DB: PDB REMARK 900 RELATED ID: 5X1D RELATED DB: PDB DBREF 5X1C A 13 490 UNP Q16555 DPYL2_HUMAN 13 490 DBREF 5X1C B 13 490 UNP Q16555 DPYL2_HUMAN 13 490 SEQADV 5X1C VAL A 7 UNP Q16555 EXPRESSION TAG SEQADV 5X1C LEU A 8 UNP Q16555 EXPRESSION TAG SEQADV 5X1C PHE A 9 UNP Q16555 EXPRESSION TAG SEQADV 5X1C GLN A 10 UNP Q16555 EXPRESSION TAG SEQADV 5X1C GLY A 11 UNP Q16555 EXPRESSION TAG SEQADV 5X1C PRO A 12 UNP Q16555 EXPRESSION TAG SEQADV 5X1C VAL B 7 UNP Q16555 EXPRESSION TAG SEQADV 5X1C LEU B 8 UNP Q16555 EXPRESSION TAG SEQADV 5X1C PHE B 9 UNP Q16555 EXPRESSION TAG SEQADV 5X1C GLN B 10 UNP Q16555 EXPRESSION TAG SEQADV 5X1C GLY B 11 UNP Q16555 EXPRESSION TAG SEQADV 5X1C PRO B 12 UNP Q16555 EXPRESSION TAG SEQRES 1 A 484 VAL LEU PHE GLN GLY PRO THR SER ASP ARG LEU LEU ILE SEQRES 2 A 484 LYS GLY GLY LYS ILE VAL ASN ASP ASP GLN SER PHE TYR SEQRES 3 A 484 ALA ASP ILE TYR MET GLU ASP GLY LEU ILE LYS GLN ILE SEQRES 4 A 484 GLY GLU ASN LEU ILE VAL PRO GLY GLY VAL LYS THR ILE SEQRES 5 A 484 GLU ALA HIS SER ARG MET VAL ILE PRO GLY GLY ILE ASP SEQRES 6 A 484 VAL HIS THR ARG PHE GLN MET PRO ASP GLN GLY MET THR SEQRES 7 A 484 SER ALA ASP ASP PHE PHE GLN GLY THR LYS ALA ALA LEU SEQRES 8 A 484 ALA GLY GLY THR THR MET ILE ILE ASP HIS VAL VAL PRO SEQRES 9 A 484 GLU PRO GLY THR SER LEU LEU ALA ALA PHE ASP GLN TRP SEQRES 10 A 484 ARG GLU TRP ALA ASP SER LYS SER CYS CYS ASP TYR SER SEQRES 11 A 484 LEU HIS VAL ASP ILE SER GLU TRP HIS LYS GLY ILE GLN SEQRES 12 A 484 GLU GLU MET GLU ALA LEU VAL LYS ASP HIS GLY VAL ASN SEQRES 13 A 484 SER PHE LEU VAL TYR MET ALA PHE LYS ASP ARG PHE GLN SEQRES 14 A 484 LEU THR ASP CYS GLN ILE TYR GLU VAL LEU SER VAL ILE SEQRES 15 A 484 ARG ASP ILE GLY ALA ILE ALA GLN VAL HIS ALA GLU ASN SEQRES 16 A 484 GLY ASP ILE ILE ALA GLU GLU GLN GLN ARG ILE LEU ASP SEQRES 17 A 484 LEU GLY ILE THR GLY PRO GLU GLY HIS VAL LEU SER ARG SEQRES 18 A 484 PRO GLU GLU VAL GLU ALA GLU ALA VAL ASN ARG ALA ILE SEQRES 19 A 484 THR ILE ALA ASN GLN THR ASN CYS PRO LEU TYR ILE THR SEQRES 20 A 484 LYS VAL MET SER LYS SER SER ALA GLU VAL ILE ALA GLN SEQRES 21 A 484 ALA ARG LYS LYS GLY THR VAL VAL TYR GLY GLU PRO ILE SEQRES 22 A 484 THR ALA SER LEU GLY THR ASP GLY SER HIS TYR TRP SER SEQRES 23 A 484 LYS ASN TRP ALA LYS ALA ALA ALA PHE VAL THR SER PRO SEQRES 24 A 484 PRO LEU SER PRO ASP PRO THR THR PRO ASP PHE LEU ASN SEQRES 25 A 484 SER LEU LEU SER CYS GLY ASP LEU GLN VAL THR GLY SER SEQRES 26 A 484 ALA HIS CYS THR PHE ASN THR ALA GLN LYS ALA VAL GLY SEQRES 27 A 484 LYS ASP ASN PHE THR LEU ILE PRO GLU GLY THR ASN GLY SEQRES 28 A 484 THR GLU GLU ARG MET SER VAL ILE TRP ASP LYS ALA VAL SEQRES 29 A 484 VAL THR GLY LYS MET ASP GLU ASN GLN PHE VAL ALA VAL SEQRES 30 A 484 THR SER THR ASN ALA ALA LYS VAL PHE ASN LEU TYR PRO SEQRES 31 A 484 ARG LYS GLY ARG ILE ALA VAL GLY SER ASP ALA ASP LEU SEQRES 32 A 484 VAL ILE TRP ASP PRO ASP SER VAL LYS THR ILE SER ALA SEQRES 33 A 484 LYS THR HIS ASN SER SER LEU GLU TYR ASN ILE PHE GLU SEQRES 34 A 484 GLY MET GLU CYS ARG GLY SER PRO LEU VAL VAL ILE SER SEQRES 35 A 484 GLN GLY LYS ILE VAL LEU GLU ASP GLY THR LEU HIS VAL SEQRES 36 A 484 THR GLU GLY SER GLY ARG TYR ILE PRO ARG LYS PRO PHE SEQRES 37 A 484 PRO ASP PHE VAL TYR LYS ARG ILE LYS ALA ARG SER ARG SEQRES 38 A 484 LEU ALA GLU SEQRES 1 B 484 VAL LEU PHE GLN GLY PRO THR SER ASP ARG LEU LEU ILE SEQRES 2 B 484 LYS GLY GLY LYS ILE VAL ASN ASP ASP GLN SER PHE TYR SEQRES 3 B 484 ALA ASP ILE TYR MET GLU ASP GLY LEU ILE LYS GLN ILE SEQRES 4 B 484 GLY GLU ASN LEU ILE VAL PRO GLY GLY VAL LYS THR ILE SEQRES 5 B 484 GLU ALA HIS SER ARG MET VAL ILE PRO GLY GLY ILE ASP SEQRES 6 B 484 VAL HIS THR ARG PHE GLN MET PRO ASP GLN GLY MET THR SEQRES 7 B 484 SER ALA ASP ASP PHE PHE GLN GLY THR LYS ALA ALA LEU SEQRES 8 B 484 ALA GLY GLY THR THR MET ILE ILE ASP HIS VAL VAL PRO SEQRES 9 B 484 GLU PRO GLY THR SER LEU LEU ALA ALA PHE ASP GLN TRP SEQRES 10 B 484 ARG GLU TRP ALA ASP SER LYS SER CYS CYS ASP TYR SER SEQRES 11 B 484 LEU HIS VAL ASP ILE SER GLU TRP HIS LYS GLY ILE GLN SEQRES 12 B 484 GLU GLU MET GLU ALA LEU VAL LYS ASP HIS GLY VAL ASN SEQRES 13 B 484 SER PHE LEU VAL TYR MET ALA PHE LYS ASP ARG PHE GLN SEQRES 14 B 484 LEU THR ASP CYS GLN ILE TYR GLU VAL LEU SER VAL ILE SEQRES 15 B 484 ARG ASP ILE GLY ALA ILE ALA GLN VAL HIS ALA GLU ASN SEQRES 16 B 484 GLY ASP ILE ILE ALA GLU GLU GLN GLN ARG ILE LEU ASP SEQRES 17 B 484 LEU GLY ILE THR GLY PRO GLU GLY HIS VAL LEU SER ARG SEQRES 18 B 484 PRO GLU GLU VAL GLU ALA GLU ALA VAL ASN ARG ALA ILE SEQRES 19 B 484 THR ILE ALA ASN GLN THR ASN CYS PRO LEU TYR ILE THR SEQRES 20 B 484 LYS VAL MET SER LYS SER SER ALA GLU VAL ILE ALA GLN SEQRES 21 B 484 ALA ARG LYS LYS GLY THR VAL VAL TYR GLY GLU PRO ILE SEQRES 22 B 484 THR ALA SER LEU GLY THR ASP GLY SER HIS TYR TRP SER SEQRES 23 B 484 LYS ASN TRP ALA LYS ALA ALA ALA PHE VAL THR SER PRO SEQRES 24 B 484 PRO LEU SER PRO ASP PRO THR THR PRO ASP PHE LEU ASN SEQRES 25 B 484 SER LEU LEU SER CYS GLY ASP LEU GLN VAL THR GLY SER SEQRES 26 B 484 ALA HIS CYS THR PHE ASN THR ALA GLN LYS ALA VAL GLY SEQRES 27 B 484 LYS ASP ASN PHE THR LEU ILE PRO GLU GLY THR ASN GLY SEQRES 28 B 484 THR GLU GLU ARG MET SER VAL ILE TRP ASP LYS ALA VAL SEQRES 29 B 484 VAL THR GLY LYS MET ASP GLU ASN GLN PHE VAL ALA VAL SEQRES 30 B 484 THR SER THR ASN ALA ALA LYS VAL PHE ASN LEU TYR PRO SEQRES 31 B 484 ARG LYS GLY ARG ILE ALA VAL GLY SER ASP ALA ASP LEU SEQRES 32 B 484 VAL ILE TRP ASP PRO ASP SER VAL LYS THR ILE SER ALA SEQRES 33 B 484 LYS THR HIS ASN SER SER LEU GLU TYR ASN ILE PHE GLU SEQRES 34 B 484 GLY MET GLU CYS ARG GLY SER PRO LEU VAL VAL ILE SER SEQRES 35 B 484 GLN GLY LYS ILE VAL LEU GLU ASP GLY THR LEU HIS VAL SEQRES 36 B 484 THR GLU GLY SER GLY ARG TYR ILE PRO ARG LYS PRO PHE SEQRES 37 B 484 PRO ASP PHE VAL TYR LYS ARG ILE LYS ALA ARG SER ARG SEQRES 38 B 484 LEU ALA GLU FORMUL 3 HOH *701(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 HIS A 145 HIS A 159 1 15 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 GLU A 229 ASN A 247 1 19 HELIX 8 AA8 SER A 257 LYS 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 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 HELIX 20 AC2 ASP B 88 GLY B 99 1 12 HELIX 21 AC3 SER B 115 SER B 131 1 17 HELIX 22 AC4 HIS B 145 HIS B 159 1 15 HELIX 23 AC5 THR B 177 GLY B 192 1 16 HELIX 24 AC6 ASN B 201 LEU B 215 1 15 HELIX 25 AC7 PRO B 220 SER B 226 1 7 HELIX 26 AC8 PRO B 228 ASN B 247 1 20 HELIX 27 AC9 SER B 257 LYS B 270 1 14 HELIX 28 AD1 ILE B 279 THR B 285 1 7 HELIX 29 AD2 ASP B 286 SER B 292 5 7 HELIX 30 AD3 ASN B 294 PHE B 301 1 8 HELIX 31 AD4 THR B 312 CYS B 323 1 12 HELIX 32 AD5 ASN B 337 ALA B 342 1 6 HELIX 33 AD6 VAL B 343 LYS B 345 5 3 HELIX 34 AD7 ASN B 347 ILE B 351 5 5 HELIX 35 AD8 GLU B 360 VAL B 370 1 11 HELIX 36 AD9 ASP B 376 SER B 385 1 10 HELIX 37 AE1 SER B 385 PHE B 392 1 8 HELIX 38 AE2 PRO B 475 ARG B 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 TYR A 36 O LYS A 43 SHEET 3 AA1 4 ARG A 16 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 TYR A 36 O LYS A 43 SHEET 3 AA2 8 ARG A 16 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 VAL A 25 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 LYS A 451 N SER A 448 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 VAL A 108 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 THR A 253 N VAL A 197 SHEET 7 AA3 7 VAL A 274 PRO A 278 1 O TYR A 275 N ILE A 252 SHEET 1 AA4 4 LEU B 41 GLY B 46 0 SHEET 2 AA4 4 SER B 30 GLU B 38 -1 N TYR B 36 O GLN B 44 SHEET 3 AA4 4 LEU B 17 VAL B 25 -1 N LEU B 17 O MET B 37 SHEET 4 AA4 4 LYS B 56 GLU B 59 1 O ILE B 58 N LYS B 20 SHEET 1 AA5 8 LEU B 41 GLY B 46 0 SHEET 2 AA5 8 SER B 30 GLU B 38 -1 N TYR B 36 O GLN B 44 SHEET 3 AA5 8 LEU B 17 VAL B 25 -1 N LEU B 17 O MET B 37 SHEET 4 AA5 8 MET B 64 PRO B 67 1 O VAL B 65 N VAL B 25 SHEET 5 AA5 8 LEU B 409 THR B 419 -1 O VAL B 410 N ILE B 66 SHEET 6 AA5 8 GLU B 438 SER B 448 -1 O LEU B 444 N ILE B 411 SHEET 7 AA5 8 LYS B 451 GLU B 455 -1 O VAL B 453 N VAL B 446 SHEET 8 AA5 8 THR B 458 LEU B 459 -1 O THR B 458 N GLU B 455 SHEET 1 AA6 7 GLY B 69 THR B 74 0 SHEET 2 AA6 7 THR B 101 VAL B 108 1 O ILE B 105 N ASP B 71 SHEET 3 AA6 7 ASP B 134 ASP B 140 1 O HIS B 138 N VAL B 108 SHEET 4 AA6 7 SER B 163 TYR B 167 1 O SER B 163 N VAL B 139 SHEET 5 AA6 7 ILE B 194 HIS B 198 1 O GLN B 196 N PHE B 164 SHEET 6 AA6 7 LEU B 250 VAL B 255 1 O TYR B 251 N VAL B 197 SHEET 7 AA6 7 VAL B 274 PRO B 278 1 O TYR B 275 N ILE B 252 SHEET 1 AA7 2 PRO B 79 ASP B 80 0 SHEET 2 AA7 2 MET B 83 THR B 84 -1 O MET B 83 N ASP B 80 CISPEP 1 GLY A 11 PRO A 12 0 7.00 CISPEP 2 SER A 304 PRO A 305 0 -6.69 CISPEP 3 TYR A 395 PRO A 396 0 3.75 CISPEP 4 SER B 304 PRO B 305 0 -8.09 CISPEP 5 TYR B 395 PRO B 396 0 1.65 CRYST1 126.687 126.687 148.219 90.00 90.00 90.00 P 42 21 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 0.007893 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007893 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006747 0.00000