HEADER TRANSFERASE 09-MAR-16 5IP4 TITLE X-RAY STRUCTURE OF THE C-TERMINAL DOMAIN OF HUMAN DOUBLECORTIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: XA4551 NANOBODY AGAINST C-DCX; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: NEURONAL MIGRATION PROTEIN DOUBLECORTIN; COMPND 7 CHAIN: D, E; COMPND 8 FRAGMENT: C-TERMINAL DOMAIN, UNP RESIDUES 251-341; COMPND 9 SYNONYM: DOUBLIN,LISSENCEPHALIN-X,LIS-X; COMPND 10 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LAMA GLAMA; SOURCE 3 ORGANISM_COMMON: LLAMA; SOURCE 4 ORGANISM_TAXID: 9844; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 9 ORGANISM_COMMON: HUMAN; SOURCE 10 ORGANISM_TAXID: 9606; SOURCE 11 GENE: DCX, DBCN, LISX; SOURCE 12 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 13 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DCX DOMAIN, UBIQUITIN-LIKE FOLD, MICROTUBULE ASSOCIATED, SIGNALING KEYWDS 2 PROTEIN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.RUF,J.BENZ,D.BURGER,B.D'ARCY,M.DEBULPAEP,P.DI LELLO,D.FRY,W.HUBER, AUTHOR 2 T.KREMER,T.LAEREMANS,H.MATILE,A.ROSS,M.G.RUDOLPH,A.C.RUFER,A.SHARMA, AUTHOR 3 M.O.STEINMETZ,J.STEYAERT,G.SCHOCH,M.STIHLE,R.THOMA REVDAT 4 10-JAN-24 5IP4 1 REMARK REVDAT 3 10-AUG-16 5IP4 1 JRNL REVDAT 2 08-JUN-16 5IP4 1 JRNL REVDAT 1 18-MAY-16 5IP4 0 JRNL AUTH D.BURGER,M.STIHLE,A.SHARMA,P.DI LELLO,J.BENZ,B.D'ARCY, JRNL AUTH 2 M.DEBULPAEP,D.FRY,W.HUBER,T.KREMER,T.LAEREMANS,H.MATILE, JRNL AUTH 3 A.ROSS,A.C.RUFER,G.SCHOCH,M.O.STEINMETZ,J.STEYAERT, JRNL AUTH 4 M.G.RUDOLPH,R.THOMA,A.RUF JRNL TITL CRYSTAL STRUCTURES OF THE HUMAN DOUBLECORTIN C- AND JRNL TITL 2 N-TERMINAL DOMAINS IN COMPLEX WITH SPECIFIC ANTIBODIES. JRNL REF J.BIOL.CHEM. V. 291 16292 2016 JRNL REFN ESSN 1083-351X JRNL PMID 27226599 JRNL DOI 10.1074/JBC.M116.726547 REMARK 2 REMARK 2 RESOLUTION. 1.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0112 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 96.0 REMARK 3 NUMBER OF REFLECTIONS : 38934 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) : 0.197 REMARK 3 R VALUE (WORKING SET) : 0.194 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2063 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) : 1.81 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.86 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2566 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 87.12 REMARK 3 BIN R VALUE (WORKING SET) : 0.4180 REMARK 3 BIN FREE R VALUE SET COUNT : 153 REMARK 3 BIN FREE R VALUE : 0.4480 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2986 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 387 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.58 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.83000 REMARK 3 B22 (A**2) : -0.37000 REMARK 3 B33 (A**2) : 0.03000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.46000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.132 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.135 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.102 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.445 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.960 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.939 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3042 ; 0.019 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4113 ; 2.121 ; 1.944 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 379 ; 6.528 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 138 ;35.236 ;23.986 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 522 ;16.083 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;25.687 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 461 ; 0.152 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2281 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 2 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 1 A 300 5 REMARK 3 1 B 1 B 300 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 436 ; 0.15 ; 0.50 REMARK 3 LOOSE POSITIONAL 1 A (A): 405 ; 0.52 ; 5.00 REMARK 3 MEDIUM THERMAL 1 A (A**2): 436 ; 1.82 ; 2.00 REMARK 3 LOOSE THERMAL 1 A (A**2): 405 ; 2.68 ; 10.00 REMARK 3 REMARK 3 NCS GROUP NUMBER : 2 REMARK 3 CHAIN NAMES : D E REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 1 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 D 1 D 500 5 REMARK 3 1 E 1 E 500 5 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 2 D (A): 320 ; 0.54 ; 0.50 REMARK 3 LOOSE POSITIONAL 2 D (A): 311 ; 0.90 ; 5.00 REMARK 3 MEDIUM THERMAL 2 D (A**2): 320 ; 5.41 ; 2.00 REMARK 3 LOOSE THERMAL 2 D (A**2): 311 ; 5.61 ; 10.00 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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: REMARK 3 HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT REMARK 3 MTRIX1 1 1.000000 0.000000 0.000000 0.00000 1 REMARK 3 MTRIX2 1 0.000000 1.000000 0.000000 0.00000 1 REMARK 3 MTRIX3 1 0.000000 0.000000 1.000000 0.00000 1 REMARK 3 MTRIX1 2 -0.953542 0.007739 -0.301161 0.89565 1 REMARK 3 MTRIX2 2 -0.006502 -0.999966 -0.005108 126.50698 1 REMARK 3 MTRIX3 2 -0.301190 -0.002913 0.953560 -7.08845 1 REMARK 4 REMARK 4 5IP4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 09-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219214. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-11 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 : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 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 : XDS (VERSION DECEMBER 6 2010) REMARK 200 DATA SCALING SOFTWARE : SADABS 2008/1 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 42622 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.810 REMARK 200 RESOLUTION RANGE LOW (A) : 44.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 3.420 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06700 REMARK 200 FOR THE DATA SET : 10.3300 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.28 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.270 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.1.4 REMARK 200 STARTING MODEL: ENSEMBLE OF 2X1O, 2X1P, 2X6M, 3DWT, 3EAK, 3G9A, REMARK 200 AND 3P0G REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.08 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEGMME, 100 MM BIS-TRIS PH 6.5, REMARK 280 VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 44.92000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.09550 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 44.92000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 43.09550 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, E 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, 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 GLN A 3 REMARK 465 SER A 113 REMARK 465 HIS A 114 REMARK 465 HIS A 115 REMARK 465 HIS A 116 REMARK 465 HIS A 117 REMARK 465 HIS A 118 REMARK 465 HIS A 119 REMARK 465 GLU A 120 REMARK 465 PRO A 121 REMARK 465 GLU A 122 REMARK 465 ALA A 123 REMARK 465 GLN B 3 REMARK 465 HIS B 114 REMARK 465 HIS B 115 REMARK 465 HIS B 116 REMARK 465 HIS B 117 REMARK 465 HIS B 118 REMARK 465 HIS B 119 REMARK 465 GLU B 120 REMARK 465 PRO B 121 REMARK 465 GLU B 122 REMARK 465 ALA B 123 REMARK 465 ALA D 251 REMARK 465 ARG D 252 REMARK 465 GLU D 253 REMARK 465 ASN D 254 REMARK 465 PRO D 335 REMARK 465 GLU D 336 REMARK 465 LYS D 337 REMARK 465 PHE D 338 REMARK 465 ARG D 339 REMARK 465 TYR D 340 REMARK 465 ALA D 341 REMARK 465 ALA E 251 REMARK 465 ARG E 252 REMARK 465 GLU E 253 REMARK 465 ASN E 254 REMARK 465 ARG E 339 REMARK 465 TYR E 340 REMARK 465 ALA E 341 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 225 O HOH A 234 1.54 REMARK 500 O HOH A 264 O HOH A 278 1.82 REMARK 500 O HOH E 440 O HOH E 447 1.95 REMARK 500 O CYS E 333 O HOH E 401 2.12 REMARK 500 O HOH A 261 O HOH A 265 2.15 REMARK 500 O HOH A 274 O HOH A 294 2.18 REMARK 500 O HOH A 282 O HOH A 289 2.19 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 ARG A 67 CD ARG A 67 NE -0.117 REMARK 500 TRP B 36 CE2 TRP B 36 CD2 0.077 REMARK 500 HIS D 321 CG HIS D 321 CD2 0.061 REMARK 500 HIS E 286 CG HIS E 286 CD2 0.057 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 ARG A 40 NE - CZ - NH1 ANGL. DEV. = 7.4 DEGREES REMARK 500 ARG A 40 NE - CZ - NH2 ANGL. DEV. = -7.7 DEGREES REMARK 500 ARG A 67 CG - CD - NE ANGL. DEV. = -12.9 DEGREES REMARK 500 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 6.9 DEGREES REMARK 500 ARG A 67 NE - CZ - NH2 ANGL. DEV. = -10.4 DEGREES REMARK 500 ARG A 72 CD - NE - CZ ANGL. DEV. = 10.8 DEGREES REMARK 500 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 9.7 DEGREES REMARK 500 ARG A 72 NE - CZ - NH2 ANGL. DEV. = -11.8 DEGREES REMARK 500 ARG B 40 CB - CG - CD ANGL. DEV. = 17.9 DEGREES REMARK 500 ARG B 40 NE - CZ - NH1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG B 40 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 ARG D 277 NE - CZ - NH2 ANGL. DEV. = -3.5 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 PRO A 43 123.96 -37.59 REMARK 500 TYR A 101 -49.31 -134.84 REMARK 500 ALA B 92 169.98 176.47 REMARK 500 TYR B 101 -47.31 -139.96 REMARK 500 VAL E 270 118.57 -17.29 REMARK 500 LYS E 274 87.33 -44.50 REMARK 500 REMARK 500 REMARK: NULL DBREF 5IP4 A 3 123 PDB 5IP4 5IP4 3 123 DBREF 5IP4 B 3 123 PDB 5IP4 5IP4 3 123 DBREF 5IP4 D 251 341 UNP O43602 DCX_HUMAN 251 341 DBREF 5IP4 E 251 341 UNP O43602 DCX_HUMAN 251 341 SEQRES 1 A 121 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 A 121 ALA GLY GLY SER LEU ARG LEU SER CYS THR ALA SER VAL SEQRES 3 A 121 ASN ILE ILE GLY GLY ASN HIS TRP ALA TRP TYR ARG GLN SEQRES 4 A 121 ALA PRO GLY GLN GLN ARG ASP LEU VAL ALA SER LEU SER SEQRES 5 A 121 ARG TYR ASN ALA ASN TYR ALA ASP SER VAL LYS GLY ARG SEQRES 6 A 121 PHE THR ILE SER ARG ASP ASN ALA LYS ASN ALA ALA TYR SEQRES 7 A 121 LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR ALA ILE SEQRES 8 A 121 TYR PHE CYS ALA LEU GLU ASN TYR TYR TRP GLY GLN GLY SEQRES 9 A 121 THR GLN VAL THR VAL SER SER HIS HIS HIS HIS HIS HIS SEQRES 10 A 121 GLU PRO GLU ALA SEQRES 1 B 121 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 B 121 ALA GLY GLY SER LEU ARG LEU SER CYS THR ALA SER VAL SEQRES 3 B 121 ASN ILE ILE GLY GLY ASN HIS TRP ALA TRP TYR ARG GLN SEQRES 4 B 121 ALA PRO GLY GLN GLN ARG ASP LEU VAL ALA SER LEU SER SEQRES 5 B 121 ARG TYR ASN ALA ASN TYR ALA ASP SER VAL LYS GLY ARG SEQRES 6 B 121 PHE THR ILE SER ARG ASP ASN ALA LYS ASN ALA ALA TYR SEQRES 7 B 121 LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR ALA ILE SEQRES 8 B 121 TYR PHE CYS ALA LEU GLU ASN TYR TYR TRP GLY GLN GLY SEQRES 9 B 121 THR GLN VAL THR VAL SER SER HIS HIS HIS HIS HIS HIS SEQRES 10 B 121 GLU PRO GLU ALA SEQRES 1 D 91 ALA ARG GLU ASN LYS ASP PHE VAL ARG PRO LYS LEU VAL SEQRES 2 D 91 THR ILE ILE ARG SER GLY VAL LYS PRO ARG LYS ALA VAL SEQRES 3 D 91 ARG VAL LEU LEU ASN LYS LYS THR ALA HIS SER PHE GLU SEQRES 4 D 91 GLN VAL LEU THR ASP ILE THR GLU ALA ILE LYS LEU GLU SEQRES 5 D 91 THR GLY VAL VAL LYS LYS LEU TYR THR LEU ASP GLY LYS SEQRES 6 D 91 GLN VAL THR CYS LEU HIS ASP PHE PHE GLY ASP ASP ASP SEQRES 7 D 91 VAL PHE ILE ALA CYS GLY PRO GLU LYS PHE ARG TYR ALA SEQRES 1 E 91 ALA ARG GLU ASN LYS ASP PHE VAL ARG PRO LYS LEU VAL SEQRES 2 E 91 THR ILE ILE ARG SER GLY VAL LYS PRO ARG LYS ALA VAL SEQRES 3 E 91 ARG VAL LEU LEU ASN LYS LYS THR ALA HIS SER PHE GLU SEQRES 4 E 91 GLN VAL LEU THR ASP ILE THR GLU ALA ILE LYS LEU GLU SEQRES 5 E 91 THR GLY VAL VAL LYS LYS LEU TYR THR LEU ASP GLY LYS SEQRES 6 E 91 GLN VAL THR CYS LEU HIS ASP PHE PHE GLY ASP ASP ASP SEQRES 7 E 91 VAL PHE ILE ALA CYS GLY PRO GLU LYS PHE ARG TYR ALA FORMUL 5 HOH *387(H2 O) HELIX 1 AA1 ASN A 74 LYS A 76 5 3 HELIX 2 AA2 LYS A 87 THR A 91 5 5 HELIX 3 AA3 ASP B 62 LYS B 65 5 4 HELIX 4 AA4 LYS B 87 THR B 91 5 5 HELIX 5 AA5 SER D 287 ILE D 299 1 13 HELIX 6 AA6 CYS D 319 PHE D 324 5 6 HELIX 7 AA7 SER E 287 LYS E 300 1 14 HELIX 8 AA8 CYS E 319 PHE E 323 5 5 HELIX 9 AA9 GLY E 334 PHE E 338 5 5 SHEET 1 AA1 4 LEU A 6 SER A 9 0 SHEET 2 AA1 4 LEU A 20 ALA A 26 -1 O SER A 23 N SER A 9 SHEET 3 AA1 4 ALA A 78 MET A 83 -1 O MET A 83 N LEU A 20 SHEET 4 AA1 4 PHE A 68 ASP A 73 -1 N ASP A 73 O ALA A 78 SHEET 1 AA2 6 GLY A 12 GLN A 15 0 SHEET 2 AA2 6 THR A 107 SER A 112 1 O GLN A 108 N GLY A 12 SHEET 3 AA2 6 ALA A 92 LEU A 98 -1 N TYR A 94 O THR A 107 SHEET 4 AA2 6 TRP A 36 GLN A 41 -1 N ALA A 37 O ALA A 97 SHEET 5 AA2 6 ASP A 48 LEU A 53 -1 O LEU A 53 N TRP A 36 SHEET 6 AA2 6 ALA A 58 TYR A 60 -1 O ASN A 59 N SER A 52 SHEET 1 AA3 4 GLY A 12 GLN A 15 0 SHEET 2 AA3 4 THR A 107 SER A 112 1 O GLN A 108 N GLY A 12 SHEET 3 AA3 4 ALA A 92 LEU A 98 -1 N TYR A 94 O THR A 107 SHEET 4 AA3 4 TYR A 102 TRP A 103 -1 O TYR A 102 N LEU A 98 SHEET 1 AA4 4 LEU B 6 SER B 9 0 SHEET 2 AA4 4 LEU B 20 ALA B 26 -1 O THR B 25 N GLN B 7 SHEET 3 AA4 4 ALA B 78 MET B 83 -1 O MET B 83 N LEU B 20 SHEET 4 AA4 4 PHE B 68 ASP B 73 -1 N THR B 69 O GLN B 82 SHEET 1 AA5 6 GLY B 12 GLN B 15 0 SHEET 2 AA5 6 THR B 107 SER B 112 1 O GLN B 108 N GLY B 12 SHEET 3 AA5 6 ALA B 92 LEU B 98 -1 N TYR B 94 O THR B 107 SHEET 4 AA5 6 TRP B 36 GLN B 41 -1 N TYR B 39 O PHE B 95 SHEET 5 AA5 6 ARG B 47 LEU B 53 -1 O ASP B 48 N ARG B 40 SHEET 6 AA5 6 ALA B 58 TYR B 60 -1 O ASN B 59 N SER B 52 SHEET 1 AA6 4 GLY B 12 GLN B 15 0 SHEET 2 AA6 4 THR B 107 SER B 112 1 O GLN B 108 N GLY B 12 SHEET 3 AA6 4 ALA B 92 LEU B 98 -1 N TYR B 94 O THR B 107 SHEET 4 AA6 4 TYR B 102 TRP B 103 -1 O TYR B 102 N LEU B 98 SHEET 1 AA7 5 ALA D 275 LEU D 280 0 SHEET 2 AA7 5 LYS D 261 SER D 268 -1 N ILE D 265 O VAL D 276 SHEET 3 AA7 5 VAL D 329 CYS D 333 1 O ALA D 332 N ILE D 266 SHEET 4 AA7 5 LEU D 309 THR D 311 -1 N TYR D 310 O ILE D 331 SHEET 5 AA7 5 GLN D 316 VAL D 317 -1 O VAL D 317 N LEU D 309 SHEET 1 AA8 4 ALA E 275 LEU E 280 0 SHEET 2 AA8 4 LYS E 261 ARG E 267 -1 N LYS E 261 O LEU E 280 SHEET 3 AA8 4 VAL E 329 CYS E 333 1 O PHE E 330 N THR E 264 SHEET 4 AA8 4 LYS E 308 THR E 311 -1 N LYS E 308 O CYS E 333 SSBOND 1 CYS A 24 CYS A 96 1555 1555 2.11 SSBOND 2 CYS B 24 CYS B 96 1555 1555 2.13 CRYST1 89.840 86.191 73.267 90.00 123.00 90.00 C 1 2 1 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 0.011131 0.000000 0.007227 0.00000 SCALE2 0.000000 0.011602 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016273 0.00000