HEADER CELL ADHESION 24-OCT-11 3UBH TITLE CRYSTAL STRUCTURE OF DROSOPHILA N-CADHERIN EC1-4 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEURAL-CADHERIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 434-851; COMPND 5 SYNONYM: CADHERIN-N, DN-CADHERIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DROSOPHILA MELANOGASTER; SOURCE 3 ORGANISM_COMMON: FRUIT FLY; SOURCE 4 ORGANISM_TAXID: 7227; SOURCE 5 GENE: CADN, CG7100; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CADHERIN, CELL ADHESION EXPDTA X-RAY DIFFRACTION AUTHOR X.JIN,M.A.WALKER,L.SHAPIRO REVDAT 6 28-FEB-24 3UBH 1 REMARK SEQADV LINK REVDAT 5 08-NOV-17 3UBH 1 REMARK REVDAT 4 12-NOV-14 3UBH 1 AUTHOR REVDAT 3 26-JUN-13 3UBH 1 JRNL REVDAT 2 18-JAN-12 3UBH 1 JRNL REVDAT 1 21-DEC-11 3UBH 0 JRNL AUTH X.JIN,M.A.WALKER,K.FELSOVALYI,J.VENDOME,F.BAHNA, JRNL AUTH 2 S.MANNEPALLI,F.COSMANESCU,G.AHLSEN,B.HONIG,L.SHAPIRO JRNL TITL CRYSTAL STRUCTURES OF DROSOPHILA N-CADHERIN ECTODOMAIN JRNL TITL 2 REGIONS REVEAL A WIDELY USED CLASS OF CA2+-FREE INTERDOMAIN JRNL TITL 3 LINKERS. JRNL REF PROC.NATL.ACAD.SCI.USA V. 109 E127 2012 JRNL REFN ISSN 0027-8424 JRNL PMID 22171007 JRNL DOI 10.1073/PNAS.1117538108 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 17118 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) : 0.209 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.276 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 919 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1089 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.58 REMARK 3 BIN R VALUE (WORKING SET) : 0.3530 REMARK 3 BIN FREE R VALUE SET COUNT : 59 REMARK 3 BIN FREE R VALUE : 0.3750 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3233 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 6 REMARK 3 SOLVENT ATOMS : 153 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 62.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.18000 REMARK 3 B22 (A**2) : 1.85000 REMARK 3 B33 (A**2) : -4.03000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.339 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.258 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 23.607 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.941 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.895 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3303 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4484 ; 1.231 ; 1.955 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 406 ; 6.125 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 169 ;35.017 ;25.030 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 557 ;17.464 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 21 ;17.329 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 498 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2557 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1374 ; 0.204 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2239 ; 0.305 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 126 ; 0.149 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 19 ; 0.174 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 48 ; 0.181 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 8 ; 0.163 ; 0.200 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): 2092 ; 0.387 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3322 ; 0.680 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1351 ; 0.968 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1162 ; 1.651 ; 4.500 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 : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 439 A 537 REMARK 3 ORIGIN FOR THE GROUP (A): -51.6065 30.1575 15.2879 REMARK 3 T TENSOR REMARK 3 T11: -0.2202 T22: -0.1458 REMARK 3 T33: -0.1275 T12: -0.0753 REMARK 3 T13: -0.0231 T23: -0.1032 REMARK 3 L TENSOR REMARK 3 L11: 4.9725 L22: 2.6136 REMARK 3 L33: 9.8475 L12: 0.4841 REMARK 3 L13: -2.0679 L23: -1.5031 REMARK 3 S TENSOR REMARK 3 S11: -0.1068 S12: -0.1582 S13: -0.0241 REMARK 3 S21: -0.0478 S22: -0.2247 S23: 0.0665 REMARK 3 S31: 0.0211 S32: -0.4412 S33: 0.3315 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 538 A 646 REMARK 3 ORIGIN FOR THE GROUP (A): -35.5982 24.4806 -27.1645 REMARK 3 T TENSOR REMARK 3 T11: -0.2090 T22: -0.2212 REMARK 3 T33: -0.1553 T12: -0.1046 REMARK 3 T13: -0.0231 T23: 0.0310 REMARK 3 L TENSOR REMARK 3 L11: 3.0496 L22: 3.0799 REMARK 3 L33: 7.6962 L12: -1.0293 REMARK 3 L13: -0.4458 L23: -0.6747 REMARK 3 S TENSOR REMARK 3 S11: -0.0210 S12: 0.0476 S13: 0.3743 REMARK 3 S21: 0.0597 S22: -0.1610 S23: -0.2879 REMARK 3 S31: -0.0036 S32: 0.0982 S33: 0.1820 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 647 A 749 REMARK 3 ORIGIN FOR THE GROUP (A): -24.2586 -3.3547 -15.8182 REMARK 3 T TENSOR REMARK 3 T11: 0.7672 T22: -0.0257 REMARK 3 T33: 0.0157 T12: 0.2618 REMARK 3 T13: 0.1062 T23: 0.1550 REMARK 3 L TENSOR REMARK 3 L11: 2.2782 L22: 7.3432 REMARK 3 L33: 20.4352 L12: -3.0602 REMARK 3 L13: 5.4018 L23: -12.2214 REMARK 3 S TENSOR REMARK 3 S11: 0.7299 S12: 0.3398 S13: -0.0695 REMARK 3 S21: -2.0007 S22: -1.0378 S23: -0.5921 REMARK 3 S31: 3.3019 S32: 1.3368 S33: 0.3079 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 750 A 850 REMARK 3 ORIGIN FOR THE GROUP (A): -12.6235 -17.1468 29.1792 REMARK 3 T TENSOR REMARK 3 T11: -0.1283 T22: 0.0456 REMARK 3 T33: -0.0291 T12: -0.1156 REMARK 3 T13: -0.0202 T23: 0.0758 REMARK 3 L TENSOR REMARK 3 L11: 3.1755 L22: 2.6550 REMARK 3 L33: 11.4157 L12: -2.6663 REMARK 3 L13: 4.3217 L23: -3.1136 REMARK 3 S TENSOR REMARK 3 S11: -0.4269 S12: -0.2001 S13: 0.5441 REMARK 3 S21: 0.1241 S22: 0.2402 S23: -0.1563 REMARK 3 S31: -0.5949 S32: -0.1434 S33: 0.1867 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 3UBH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 26-OCT-11. REMARK 100 THE DEPOSITION ID IS D_1000068545. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-MAR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9788 REMARK 200 MONOCHROMATOR : SI 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 18088 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL 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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.54 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.37 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 9% PEG 3350, 0.05M L-PROLINE, 0.1M REMARK 280 HEPES, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 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 -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 40.74950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 63.32800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 40.74950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 63.32800 REMARK 290 SMTRY3 4 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 300 REMARK: MONOMER 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 433 REMARK 465 ARG A 434 REMARK 465 ARG A 435 REMARK 465 VAL A 436 REMARK 465 THR A 437 REMARK 465 MET A 515 REMARK 465 GLY A 516 REMARK 465 ASP A 628 REMARK 465 ASP A 629 REMARK 465 LYS A 851 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 ARG A 438 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 596 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 665 CG CD CE NZ REMARK 470 ARG A 684 CG CD NE CZ NH1 NH2 REMARK 470 LYS A 710 CG CD CE NZ REMARK 470 GLN A 814 CG CD OE1 NE2 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 682 CD GLU A 682 OE1 0.149 REMARK 500 GLU A 682 CD GLU A 682 OE2 0.088 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 LYS A 492 -82.93 -98.41 REMARK 500 ASN A 518 -1.36 86.03 REMARK 500 ASN A 537 86.34 -66.29 REMARK 500 ASP A 667 -7.88 75.60 REMARK 500 ASP A 785 -173.43 -68.57 REMARK 500 ASP A 799 4.40 -65.87 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 852 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 450 OE2 REMARK 620 2 ASP A 496 OD1 90.2 REMARK 620 3 GLU A 498 OE1 73.1 84.5 REMARK 620 4 ASP A 538 OD2 86.3 166.4 106.9 REMARK 620 5 ASP A 538 OD1 78.5 146.8 62.3 44.8 REMARK 620 6 GLU A 539 OE2 153.6 112.4 94.7 74.7 75.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 853 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 450 OE1 REMARK 620 2 GLU A 498 OE2 117.5 REMARK 620 3 GLU A 498 OE1 88.9 52.1 REMARK 620 4 ASP A 535 OD1 84.3 79.7 120.3 REMARK 620 5 VAL A 536 O 79.9 159.5 144.4 92.4 REMARK 620 6 ASP A 538 OD1 80.2 117.3 70.5 161.0 74.3 REMARK 620 7 ASP A 573 OD2 156.5 85.1 101.8 107.3 79.3 83.7 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 854 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 537 OD1 REMARK 620 2 GLU A 539 O 112.0 REMARK 620 3 ASP A 571 OD2 157.6 85.2 REMARK 620 4 ASP A 571 OD1 132.7 97.2 54.0 REMARK 620 5 ASP A 573 OD1 72.3 74.1 128.1 81.6 REMARK 620 6 ASP A 622 OD2 77.3 151.1 80.9 94.9 133.9 REMARK 620 7 GLN A 633 OE1 71.7 72.6 101.9 155.2 115.5 85.6 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 855 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 662 OE1 REMARK 620 2 ASP A 713 OD2 92.3 REMARK 620 3 GLU A 715 OE1 81.8 98.9 REMARK 620 4 ASP A 751 OD2 87.2 161.5 99.3 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 856 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 662 OE2 REMARK 620 2 GLU A 715 OE1 86.2 REMARK 620 3 GLU A 715 OE2 111.3 51.6 REMARK 620 4 ASP A 748 OD1 98.4 133.8 84.8 REMARK 620 5 VAL A 749 O 76.9 146.3 162.1 78.2 REMARK 620 6 ASP A 751 OD1 79.5 71.8 120.0 154.4 76.5 REMARK 620 7 ASP A 785 OD1 150.3 93.3 91.1 103.1 87.6 72.2 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 857 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASN A 750 OD1 REMARK 620 2 ASN A 752 O 99.2 REMARK 620 3 ASP A 783 OD2 155.2 94.1 REMARK 620 4 ASP A 783 OD1 149.9 86.7 51.2 REMARK 620 5 ASP A 785 OD2 76.0 78.4 127.5 76.4 REMARK 620 6 ASN A 789 O 86.5 174.2 80.9 87.9 102.3 REMARK 620 7 ASP A 832 OD2 73.7 89.7 85.6 136.2 145.1 92.8 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 852 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 853 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 854 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 855 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 856 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 857 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3UBF RELATED DB: PDB REMARK 900 RELATED ID: 3UBG RELATED DB: PDB DBREF 3UBH A 434 851 UNP O15943 CADN_DROME 434 851 SEQADV 3UBH SER A 433 UNP O15943 EXPRESSION TAG SEQRES 1 A 419 SER ARG ARG VAL THR ARG ALA VAL ARG PRO THR LYS ARG SEQRES 2 A 419 ILE GLU PHE THR GLU ALA ASP GLY ASP THR GLU GLY LYS SEQRES 3 A 419 SER VAL PHE GLN LEU GLU LYS GLU THR ASP LYS GLU THR SEQRES 4 A 419 PHE LYS ILE ARG ASP ASP ASN PRO TRP VAL THR VAL GLU SEQRES 5 A 419 THR ASN GLY ALA VAL ARG VAL LYS LYS LYS TRP ASP TYR SEQRES 6 A 419 GLU GLU LEU GLY PRO GLU LYS THR ILE ASP PHE TRP VAL SEQRES 7 A 419 ILE ILE THR ASN MET GLY HIS ASN ALA GLY ILE LYS TYR SEQRES 8 A 419 THR ASP ASN GLN ARG VAL ILE ILE LEU VAL LYS ASP VAL SEQRES 9 A 419 ASN ASP GLU PRO PRO TYR PHE ILE ASN ARG PRO LEU PRO SEQRES 10 A 419 MET GLN ALA VAL VAL GLN LEU ASN ALA PRO PRO ASN THR SEQRES 11 A 419 PRO VAL PHE THR LEU GLN ALA ARG ASP PRO ASP THR ASP SEQRES 12 A 419 HIS ASN ILE HIS TYR PHE ILE VAL ARG ASP ARG THR GLY SEQRES 13 A 419 GLY ARG PHE GLU VAL ASP GLU ARG SER GLY VAL VAL ARG SEQRES 14 A 419 THR ARG GLY THR ASP LEU PHE GLN LEU ASP MET GLU TYR SEQRES 15 A 419 VAL LEU TYR VAL LYS ALA GLU ASP GLN ASN GLY LYS VAL SEQRES 16 A 419 ASP ASP ARG ARG PHE GLN SER THR PRO GLU GLU ARG LEU SEQRES 17 A 419 SER ILE VAL GLY GLY LYS ARG ALA PRO GLN PHE TYR MET SEQRES 18 A 419 PRO SER TYR GLU ALA GLU ILE PRO GLU ASN GLN LYS LYS SEQRES 19 A 419 ASP SER ASP ILE ILE SER ILE LYS ALA LYS SER PHE ALA SEQRES 20 A 419 ASP ARG GLU ILE ARG TYR THR LEU LYS ALA GLN GLY GLN SEQRES 21 A 419 GLY ALA GLY THR PHE ASN ILE GLY PRO THR SER GLY ILE SEQRES 22 A 419 VAL LYS LEU ALA LYS GLU LEU ASP PHE GLU ASP LEU ARG SEQRES 23 A 419 GLN PRO HIS VAL TYR SER LEU ILE VAL THR ALA THR GLU SEQRES 24 A 419 ASP SER GLY GLY PHE SER THR SER VAL ASP LEU THR ILE SEQRES 25 A 419 ARG VAL THR ASP VAL ASN ASP ASN ALA PRO LYS PHE GLU SEQRES 26 A 419 LEU PRO ASP TYR GLN ALA HIS ASN VAL ASP GLU ASP ILE SEQRES 27 A 419 PRO LEU GLY THR SER ILE LEU ARG VAL LYS ALA MET ASP SEQRES 28 A 419 SER ASP SER GLY SER ASN ALA GLU ILE GLU TYR LEU VAL SEQRES 29 A 419 SER ASP ASP HIS PHE ALA VAL ASP SER ASN GLY ILE ILE SEQRES 30 A 419 VAL ASN ASN LYS GLN LEU ASP ALA ASP ASN ASN ASN ALA SEQRES 31 A 419 TYR TYR GLU PHE ILE VAL THR ALA LYS ASP LYS GLY GLU SEQRES 32 A 419 PRO PRO LYS SER GLY VAL ALA THR VAL ARG VAL TYR THR SEQRES 33 A 419 LYS ASN LYS HET CA A 852 1 HET CA A 853 1 HET CA A 854 1 HET CA A 855 1 HET CA A 856 1 HET CA A 857 1 HETNAM CA CALCIUM ION FORMUL 2 CA 6(CA 2+) FORMUL 8 HOH *153(H2 O) HELIX 1 1 ALA A 451 ASP A 454 5 4 HELIX 2 2 ASP A 496 LEU A 500 5 5 HELIX 3 3 SER A 786 ALA A 790 5 5 SHEET 1 A 4 VAL A 440 THR A 449 0 SHEET 2 A 4 TYR A 523 LYS A 534 1 O LYS A 534 N PHE A 448 SHEET 3 A 4 THR A 505 ASN A 514 -1 N PHE A 508 O VAL A 529 SHEET 4 A 4 THR A 471 ILE A 474 -1 N LYS A 473 O ILE A 511 SHEET 1 B 3 SER A 459 GLN A 462 0 SHEET 2 B 3 ALA A 488 VAL A 491 -1 O VAL A 489 N PHE A 461 SHEET 3 B 3 VAL A 481 VAL A 483 -1 N THR A 482 O ARG A 490 SHEET 1 C 2 TYR A 542 PHE A 543 0 SHEET 2 C 2 ALA A 569 ARG A 570 -1 O ARG A 570 N TYR A 542 SHEET 1 D 4 GLN A 551 VAL A 554 0 SHEET 2 D 4 GLU A 638 GLY A 644 1 O SER A 641 N ALA A 552 SHEET 3 D 4 GLU A 613 LYS A 626 -1 N LEU A 616 O LEU A 640 SHEET 4 D 4 ILE A 578 ASP A 585 -1 N ARG A 584 O TYR A 617 SHEET 1 E 4 GLN A 551 VAL A 554 0 SHEET 2 E 4 GLU A 638 GLY A 644 1 O SER A 641 N ALA A 552 SHEET 3 E 4 GLU A 613 LYS A 626 -1 N LEU A 616 O LEU A 640 SHEET 4 E 4 PHE A 632 SER A 634 -1 O GLN A 633 N GLY A 625 SHEET 1 F 3 PRO A 563 THR A 566 0 SHEET 2 F 3 VAL A 599 THR A 602 -1 O VAL A 600 N PHE A 565 SHEET 3 F 3 PHE A 591 VAL A 593 -1 N GLU A 592 O ARG A 601 SHEET 1 G 2 GLN A 650 PHE A 651 0 SHEET 2 G 2 ALA A 675 LYS A 676 -1 O LYS A 676 N GLN A 650 SHEET 1 H 4 TYR A 656 PRO A 661 0 SHEET 2 H 4 SER A 737 THR A 747 1 O THR A 743 N TYR A 656 SHEET 3 H 4 VAL A 722 THR A 730 -1 N TYR A 723 O ILE A 744 SHEET 4 H 4 ARG A 684 ALA A 689 -1 N ARG A 684 O THR A 730 SHEET 1 I 3 ASP A 669 SER A 672 0 SHEET 2 I 3 ILE A 705 LEU A 708 -1 O VAL A 706 N ILE A 671 SHEET 3 I 3 PHE A 697 ILE A 699 -1 N ASN A 698 O LYS A 707 SHEET 1 J 2 LYS A 755 PHE A 756 0 SHEET 2 J 2 ALA A 781 MET A 782 -1 O MET A 782 N LYS A 755 SHEET 1 K 4 ASP A 760 ASP A 767 0 SHEET 2 K 4 SER A 839 LYS A 849 1 O THR A 843 N TYR A 761 SHEET 3 K 4 TYR A 823 ASP A 832 -1 N PHE A 826 O VAL A 844 SHEET 4 K 4 ILE A 792 VAL A 796 -1 N GLU A 793 O LYS A 831 SHEET 1 L 3 SER A 775 ARG A 778 0 SHEET 2 L 3 ILE A 808 ASN A 811 -1 O ILE A 809 N LEU A 777 SHEET 3 L 3 PHE A 801 VAL A 803 -1 N ALA A 802 O VAL A 810 LINK OE2 GLU A 450 CA CA A 852 1555 1555 2.07 LINK OE1 GLU A 450 CA CA A 853 1555 1555 2.82 LINK OD1 ASP A 496 CA CA A 852 1555 1555 2.25 LINK OE1 GLU A 498 CA CA A 852 1555 1555 2.46 LINK OE2 GLU A 498 CA CA A 853 1555 1555 2.34 LINK OE1 GLU A 498 CA CA A 853 1555 1555 2.60 LINK OD1 ASP A 535 CA CA A 853 1555 1555 2.33 LINK O VAL A 536 CA CA A 853 1555 1555 2.13 LINK OD1 ASN A 537 CA CA A 854 1555 1555 2.44 LINK OD2 ASP A 538 CA CA A 852 1555 1555 2.42 LINK OD1 ASP A 538 CA CA A 852 1555 1555 3.07 LINK OD1 ASP A 538 CA CA A 853 1555 1555 2.43 LINK OE2 GLU A 539 CA CA A 852 1555 1555 2.26 LINK O GLU A 539 CA CA A 854 1555 1555 2.37 LINK OD2 ASP A 571 CA CA A 854 1555 1555 2.30 LINK OD1 ASP A 571 CA CA A 854 1555 1555 2.50 LINK OD2 ASP A 573 CA CA A 853 1555 1555 2.29 LINK OD1 ASP A 573 CA CA A 854 1555 1555 2.57 LINK OD2 ASP A 622 CA CA A 854 1555 1555 2.27 LINK OE1 GLN A 633 CA CA A 854 1555 1555 2.44 LINK OE1 GLU A 662 CA CA A 855 1555 1555 2.58 LINK OE2 GLU A 662 CA CA A 856 1555 1555 2.43 LINK OD2 ASP A 713 CA CA A 855 1555 1555 2.14 LINK OE1 GLU A 715 CA CA A 855 1555 1555 2.54 LINK OE1 GLU A 715 CA CA A 856 1555 1555 2.49 LINK OE2 GLU A 715 CA CA A 856 1555 1555 2.57 LINK OD1 ASP A 748 CA CA A 856 1555 1555 2.20 LINK O VAL A 749 CA CA A 856 1555 1555 2.36 LINK OD1 ASN A 750 CA CA A 857 1555 1555 2.32 LINK OD2 ASP A 751 CA CA A 855 1555 1555 2.18 LINK OD1 ASP A 751 CA CA A 856 1555 1555 2.50 LINK O ASN A 752 CA CA A 857 1555 1555 2.32 LINK OD2 ASP A 783 CA CA A 857 1555 1555 2.37 LINK OD1 ASP A 783 CA CA A 857 1555 1555 2.67 LINK OD1 ASP A 785 CA CA A 856 1555 1555 2.45 LINK OD2 ASP A 785 CA CA A 857 1555 1555 2.35 LINK O ASN A 789 CA CA A 857 1555 1555 2.28 LINK OD2 ASP A 832 CA CA A 857 1555 1555 2.70 CISPEP 1 ARG A 546 PRO A 547 0 -3.38 CISPEP 2 LEU A 548 PRO A 549 0 -1.68 CISPEP 3 GLN A 690 GLY A 691 0 -13.30 CISPEP 4 GLU A 835 PRO A 836 0 3.58 SITE 1 AC1 5 GLU A 450 ASP A 496 GLU A 498 ASP A 538 SITE 2 AC1 5 GLU A 539 SITE 1 AC2 6 GLU A 450 GLU A 498 ASP A 535 VAL A 536 SITE 2 AC2 6 ASP A 538 ASP A 573 SITE 1 AC3 6 ASN A 537 GLU A 539 ASP A 571 ASP A 573 SITE 2 AC3 6 ASP A 622 GLN A 633 SITE 1 AC4 4 GLU A 662 ASP A 713 GLU A 715 ASP A 751 SITE 1 AC5 6 GLU A 662 GLU A 715 ASP A 748 VAL A 749 SITE 2 AC5 6 ASP A 751 ASP A 785 SITE 1 AC6 6 ASN A 750 ASN A 752 ASP A 783 ASP A 785 SITE 2 AC6 6 ASN A 789 ASP A 832 CRYST1 81.499 126.656 62.009 90.00 90.00 90.00 P 21 21 2 4 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 0.012270 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007895 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016127 0.00000