HEADER IMMUNE SYSTEM 14-MAR-16 5IRN TITLE CRYSTAL STRUCTURE OF RABBIT NOD2 IN AN ADP-BOUND STATE (CRYSTAL FORM1) COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 194-1020; COMPND 5 SYNONYM: NOD2; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ORYCTOLAGUS CUNICULUS; SOURCE 3 ORGANISM_COMMON: RABBIT; SOURCE 4 ORGANISM_TAXID: 9986; SOURCE 5 GENE: NOD2; SOURCE 6 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 7 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: BACULOVIRUS KEYWDS IMMUNE SYSTEM, NOD2, INNATE IMMUNITY EXPDTA X-RAY DIFFRACTION AUTHOR S.MAEKAWA,U.OHTO,T.SHIMIZU REVDAT 3 20-MAR-24 5IRN 1 REMARK REVDAT 2 19-FEB-20 5IRN 1 REMARK REVDAT 1 29-JUN-16 5IRN 0 JRNL AUTH S.MAEKAWA,U.OHTO,T.SHIBATA,K.MIYAKE,T.SHIMIZU JRNL TITL CRYSTAL STRUCTURE OF NOD2 AND ITS IMPLICATIONS IN HUMAN JRNL TITL 2 DISEASE. JRNL REF NAT COMMUN V. 7 11813 2016 JRNL REFN ESSN 2041-1723 JRNL PMID 27283905 JRNL DOI 10.1038/NCOMMS11813 REMARK 2 REMARK 2 RESOLUTION. 2.34 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.34 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 92.70 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.8 REMARK 3 NUMBER OF REFLECTIONS : 57509 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) : 0.203 REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.236 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3063 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) : 2.34 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.40 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3020 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 66.30 REMARK 3 BIN R VALUE (WORKING SET) : 0.3270 REMARK 3 BIN FREE R VALUE SET COUNT : 185 REMARK 3 BIN FREE R VALUE : 0.3790 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5833 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 47 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 76.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.02000 REMARK 3 B22 (A**2) : -0.54000 REMARK 3 B33 (A**2) : 0.56000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.206 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.185 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.135 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.943 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5969 ; 0.012 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 5780 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8082 ; 1.507 ; 1.970 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13227 ; 0.992 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 738 ; 6.053 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 273 ;38.627 ;23.883 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1026 ;15.538 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 41 ;17.452 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 933 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6741 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1423 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2976 ; 5.010 ; 6.717 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2975 ; 5.010 ; 6.717 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3706 ; 7.018 ;10.036 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3707 ; 7.017 ;10.037 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2993 ; 5.511 ; 7.302 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2994 ; 5.510 ; 7.301 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4377 ; 8.058 ;10.733 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 6430 ;10.265 ;52.202 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 6428 ;10.264 ;52.202 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 : 1 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 195 A 1020 REMARK 3 ORIGIN FOR THE GROUP (A): 51.4312 83.6304 112.0191 REMARK 3 T TENSOR REMARK 3 T11: 0.0416 T22: 0.1246 REMARK 3 T33: 0.0103 T12: 0.0084 REMARK 3 T13: 0.0026 T23: -0.0292 REMARK 3 L TENSOR REMARK 3 L11: 0.1590 L22: 0.2946 REMARK 3 L33: 0.1308 L12: -0.0508 REMARK 3 L13: -0.1071 L23: 0.0454 REMARK 3 S TENSOR REMARK 3 S11: -0.0043 S12: -0.1207 S13: 0.0208 REMARK 3 S21: -0.0178 S22: -0.0028 S23: -0.0094 REMARK 3 S31: 0.0050 S32: 0.0406 S33: 0.0071 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 5IRN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 17-MAR-16. REMARK 100 THE DEPOSITION ID IS D_1000219277. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 11-OCT-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 : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 57510 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 92.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.6 REMARK 200 DATA REDUNDANCY : 6.700 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.7000 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: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 71.09 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 4.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 5% PEG 20000, 5% MPD, 100 MM HEPES PH REMARK 280 7.8, 500 MM NACL, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 38.90750 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 92.69650 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 53.08100 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 92.69650 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 38.90750 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 53.08100 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 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 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 GLY A 191 REMARK 465 PRO A 192 REMARK 465 GLU A 193 REMARK 465 PHE A 194 REMARK 465 SER A 218 REMARK 465 THR A 219 REMARK 465 TYR A 220 REMARK 465 ASP A 221 REMARK 465 GLY A 222 REMARK 465 ALA A 223 REMARK 465 GLU A 224 REMARK 465 GLU A 242 REMARK 465 VAL A 243 REMARK 465 GLY A 244 REMARK 465 MET A 245 REMARK 465 ALA A 246 REMARK 465 GLY A 247 REMARK 465 PRO A 248 REMARK 465 LEU A 249 REMARK 465 HIS A 250 REMARK 465 LYS A 251 REMARK 465 SER A 252 REMARK 465 PRO A 253 REMARK 465 PRO A 264 REMARK 465 ASN A 265 REMARK 465 GLY A 266 REMARK 465 HIS A 267 REMARK 465 LEU A 268 REMARK 465 ASN A 269 REMARK 465 SER A 506 REMARK 465 LEU A 507 REMARK 465 PRO A 508 REMARK 465 ASP A 509 REMARK 465 SER A 510 REMARK 465 ALA A 511 REMARK 465 SER A 512 REMARK 465 GLN A 513 REMARK 465 GLY A 514 REMARK 465 LEU A 515 REMARK 465 GLY A 516 REMARK 465 PRO A 517 REMARK 465 ALA A 568 REMARK 465 GLN A 569 REMARK 465 GLY A 570 REMARK 465 VAL A 571 REMARK 465 VAL A 572 REMARK 465 PRO A 573 REMARK 465 GLY A 574 REMARK 465 SER A 575 REMARK 465 THR A 576 REMARK 465 ARG A 613 REMARK 465 ARG A 614 REMARK 465 PRO A 615 REMARK 465 GLY A 616 REMARK 465 SER A 617 REMARK 465 SER A 618 REMARK 465 PRO A 619 REMARK 465 LEU A 620 REMARK 465 SER A 621 REMARK 465 ARG A 622 REMARK 465 LEU A 623 REMARK 465 LEU A 624 REMARK 465 PRO A 625 REMARK 465 ARG A 626 REMARK 465 LEU A 627 REMARK 465 CYS A 628 REMARK 465 VAL A 629 REMARK 465 GLN A 630 REMARK 465 GLY A 631 REMARK 465 SER A 632 REMARK 465 GLU A 633 REMARK 465 HIS A 634 REMARK 465 LYS A 635 REMARK 465 PRO A 703 REMARK 465 PRO A 704 REMARK 465 ALA A 705 REMARK 465 VAL A 706 REMARK 465 PRO A 707 REMARK 465 GLY A 708 REMARK 465 GLU A 709 REMARK 465 ALA A 710 REMARK 465 LYS A 711 REMARK 465 SER A 712 REMARK 465 MET A 713 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 GLU A 270 CG CD OE1 OE2 REMARK 470 LYS A 397 CG CD CE NZ REMARK 470 PHE A 413 CG CD1 CD2 CE1 CE2 CZ REMARK 470 LYS A 416 CG CD CE NZ 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 658 CA - CB - CG ANGL. DEV. = 16.6 DEGREES REMARK 500 ARG A 684 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 724 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ARG A 857 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 857 NE - CZ - NH2 ANGL. DEV. = -3.8 DEGREES REMARK 500 ARG A 876 NE - CZ - NH1 ANGL. DEV. = 3.1 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 ALA A 197 170.35 -59.78 REMARK 500 ALA A 272 -167.98 -104.90 REMARK 500 CYS A 333 -68.59 -156.77 REMARK 500 HIS A 374 92.62 -161.31 REMARK 500 THR A 381 -179.45 -178.78 REMARK 500 ASN A 398 -10.07 83.05 REMARK 500 ASP A 483 45.29 -98.21 REMARK 500 GLN A 554 32.38 79.00 REMARK 500 HIS A 779 64.06 64.61 REMARK 500 ASN A 780 -159.94 -144.24 REMARK 500 ASN A 805 15.98 -142.16 REMARK 500 ASN A 833 -149.56 -130.68 REMARK 500 ASN A 861 -164.89 -121.99 REMARK 500 TRP A 887 123.49 -38.26 REMARK 500 ASN A 889 -169.84 -78.29 REMARK 500 ASN A 945 -161.86 -101.78 REMARK 500 GLN A 948 171.29 67.13 REMARK 500 SER A 964 -33.50 -133.33 REMARK 500 ASP A1015 116.88 -30.99 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ADP A 1101 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5IRM RELATED DB: PDB REMARK 900 RELATED ID: 5IRL RELATED DB: PDB DBREF 5IRN A 194 1020 UNP G1T469 G1T469_RABIT 194 1020 SEQADV 5IRN GLY A 191 UNP G1T469 EXPRESSION TAG SEQADV 5IRN PRO A 192 UNP G1T469 EXPRESSION TAG SEQADV 5IRN GLU A 193 UNP G1T469 EXPRESSION TAG SEQRES 1 A 830 GLY PRO GLU PHE GLU ALA ALA ALA CYS LYS LYS TYR MET SEQRES 2 A 830 SER LYS LEU ARG THR ILE VAL ALA ALA GLN SER ARG PHE SEQRES 3 A 830 LEU SER THR TYR ASP GLY ALA GLU ASN LEU CYS LEU GLU SEQRES 4 A 830 ASP ILE TYR THR GLU ASN THR LEU GLU VAL ARG THR GLU SEQRES 5 A 830 VAL GLY MET ALA GLY PRO LEU HIS LYS SER PRO ALA ALA SEQRES 6 A 830 LEU GLY LEU GLU GLU LEU PHE SER PRO ASN GLY HIS LEU SEQRES 7 A 830 ASN GLU ASP ALA ASP THR VAL LEU VAL VAL GLY GLU ALA SEQRES 8 A 830 GLY SER GLY LYS SER THR LEU LEU GLN GLN VAL HIS LEU SEQRES 9 A 830 LEU TRP ALA THR GLY GLN ASP PHE GLN GLU PHE LEU PHE SEQRES 10 A 830 VAL PHE PRO PHE SER CYS ARG GLN LEU GLN CYS VAL ALA SEQRES 11 A 830 ARG PRO LEU SER VAL MET THR LEU LEU PHE GLU HIS CYS SEQRES 12 A 830 CYS TRP PRO ASP VAL GLY GLN GLN ASP VAL PHE GLN PHE SEQRES 13 A 830 LEU LEU ASP HIS PRO ASP ARG ILE LEU LEU THR PHE ASP SEQRES 14 A 830 GLY PHE ASP GLU PHE LYS PHE LYS PHE THR ASP HIS GLU SEQRES 15 A 830 ARG HIS CYS SER PRO THR ASP PRO THR SER VAL GLN THR SEQRES 16 A 830 LEU LEU PHE ASN LEU LEU GLN GLY ASN LEU LEU LYS ASN SEQRES 17 A 830 ALA ARG LYS VAL LEU THR SER ARG PRO ASP ALA VAL SER SEQRES 18 A 830 ALA PHE LEU ARG LYS TYR VAL ARG THR GLU PHE ASN LEU SEQRES 19 A 830 LYS GLY PHE SER GLU GLU GLY ILE GLU LEU TYR LEU ARG SEQRES 20 A 830 LYS CYS HIS ARG GLU PRO GLY VAL ALA ASP ARG LEU ILE SEQRES 21 A 830 HIS LEU LEU GLN THR THR SER ALA LEU HIS GLY LEU CYS SEQRES 22 A 830 HIS LEU PRO VAL PHE SER TRP MET VAL SER LYS CYS HIS SEQRES 23 A 830 GLN GLU LEU LEU LEU GLN ASP GLY GLY SER PRO LYS THR SEQRES 24 A 830 THR THR ASP MET TYR LEU LEU ILE LEU GLN HIS PHE LEU SEQRES 25 A 830 ARG HIS ALA SER LEU PRO ASP SER ALA SER GLN GLY LEU SEQRES 26 A 830 GLY PRO SER LEU LEU GLN GLY ARG LEU PRO THR LEU LEU SEQRES 27 A 830 ARG LEU GLY GLN LEU ALA LEU TRP GLY LEU GLY MET CYS SEQRES 28 A 830 CYS TYR VAL PHE SER ALA GLN GLN LEU GLN ALA ALA GLN SEQRES 29 A 830 VAL ASP PRO ASP ASP ILE SER LEU GLY PHE LEU VAL GLN SEQRES 30 A 830 ALA GLN GLY VAL VAL PRO GLY SER THR ALA PRO LEU GLU SEQRES 31 A 830 PHE LEU HIS ILE THR PHE GLN CYS PHE LEU ALA ALA PHE SEQRES 32 A 830 TYR LEU VAL LEU SER THR ASP VAL PRO THR ALA SER LEU SEQRES 33 A 830 ARG TYR LEU PHE ASN CYS ARG ARG PRO GLY SER SER PRO SEQRES 34 A 830 LEU SER ARG LEU LEU PRO ARG LEU CYS VAL GLN GLY SER SEQRES 35 A 830 GLU HIS LYS GLU SER THR VAL ALA ALA LEU LEU GLN LYS SEQRES 36 A 830 THR GLU PRO HIS ASN LEU GLN ILE THR ALA ALA PHE LEU SEQRES 37 A 830 ALA GLY LEU LEU SER ARG GLU HIS ARG ASP LEU LEU ALA SEQRES 38 A 830 ALA CYS GLN ALA SER GLU ARG SER LEU LEU ARG ARG ARG SEQRES 39 A 830 ALA CYS ALA ARG TRP CYS LEU ALA ARG SER LEU HIS LYS SEQRES 40 A 830 HIS PHE ARG SER ILE PRO PRO ALA VAL PRO GLY GLU ALA SEQRES 41 A 830 LYS SER MET HIS ALA MET PRO GLY PHE LEU TRP LEU ILE SEQRES 42 A 830 ARG SER LEU TYR GLU MET GLN GLU GLU ARG LEU ALA GLN SEQRES 43 A 830 GLU ALA VAL ARG GLY LEU ASN VAL GLU HIS LEU LYS LEU SEQRES 44 A 830 THR PHE CYS GLY VAL GLY PRO ALA GLU CYS ALA ALA LEU SEQRES 45 A 830 ALA PHE VAL LEU ARG HIS LEU ARG ARG PRO VAL ALA LEU SEQRES 46 A 830 GLN LEU ASP HIS ASN SER VAL GLY ASP ILE GLY VAL GLU SEQRES 47 A 830 GLN LEU LEU PRO CYS LEU GLY ALA CYS LYS ALA LEU TYR SEQRES 48 A 830 LEU ARG ASP ASN ASN ILE SER ASP ARG GLY ILE CYS LYS SEQRES 49 A 830 LEU ILE GLU HIS ALA LEU HIS CYS GLU GLN LEU GLN LYS SEQRES 50 A 830 LEU ALA LEU PHE ASN ASN LYS LEU THR ASP GLY CYS ALA SEQRES 51 A 830 HIS SER VAL ALA GLN LEU LEU ALA CYS LYS GLN ASN PHE SEQRES 52 A 830 LEU ALA LEU ARG LEU GLY ASN ASN HIS ILE THR ALA GLU SEQRES 53 A 830 GLY ALA GLN VAL LEU ALA GLU GLY LEU ARG ASP ASN SER SEQRES 54 A 830 SER LEU GLN PHE LEU GLY PHE TRP GLY ASN LYS VAL GLY SEQRES 55 A 830 ASP LYS GLY ALA GLN ALA LEU ALA GLU ALA LEU SER ASP SEQRES 56 A 830 HIS GLN SER LEU LYS TRP LEU SER LEU VAL GLY ASN ASN SEQRES 57 A 830 ILE GLY SER VAL GLY ALA GLN ALA LEU ALA SER MET LEU SEQRES 58 A 830 GLU LYS ASN VAL ALA LEU GLU GLU LEU CYS LEU GLU GLU SEQRES 59 A 830 ASN HIS LEU GLN ASP ALA GLY VAL CYS SER LEU ALA GLU SEQRES 60 A 830 GLY LEU LYS ARG ASN SER SER LEU LYS VAL LEU LYS LEU SEQRES 61 A 830 SER ASN ASN CYS ILE THR PHE VAL GLY ALA GLU ALA LEU SEQRES 62 A 830 LEU GLN ALA LEU ALA SER ASN ASP THR ILE LEU GLU VAL SEQRES 63 A 830 TRP LEU ARG GLY ASN PRO PHE SER PRO GLU GLU MET GLU SEQRES 64 A 830 ALA LEU SER HIS ARG ASP SER ARG LEU LEU LEU HET ADP A1101 27 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 HOH *47(H2 O) HELIX 1 AA1 ALA A 197 ARG A 215 1 19 HELIX 2 AA2 CYS A 227 TYR A 232 1 6 HELIX 3 AA3 GLY A 257 LEU A 261 5 5 HELIX 4 AA4 GLY A 284 THR A 298 1 15 HELIX 5 AA5 CYS A 313 CYS A 318 1 6 HELIX 6 AA6 SER A 324 HIS A 332 1 9 HELIX 7 AA7 GLY A 339 HIS A 350 1 12 HELIX 8 AA8 GLY A 360 PHE A 364 5 5 HELIX 9 AA9 SER A 382 GLN A 392 1 11 HELIX 10 AB1 SER A 411 LYS A 416 1 6 HELIX 11 AB2 SER A 428 HIS A 440 1 13 HELIX 12 AB3 GLY A 444 THR A 456 1 13 HELIX 13 AB4 THR A 456 CYS A 463 1 8 HELIX 14 AB5 LEU A 465 CYS A 475 1 11 HELIX 15 AB6 CYS A 475 GLN A 482 1 8 HELIX 16 AB7 THR A 489 HIS A 504 1 16 HELIX 17 AB8 LEU A 519 ARG A 523 1 5 HELIX 18 AB9 ARG A 523 MET A 540 1 18 HELIX 19 AC1 SER A 546 ALA A 553 1 8 HELIX 20 AC2 ASP A 556 SER A 561 1 6 HELIX 21 AC3 HIS A 583 SER A 598 1 16 HELIX 22 AC4 PRO A 602 PHE A 610 5 9 HELIX 23 AC5 SER A 637 THR A 646 1 10 HELIX 24 AC6 GLU A 647 LEU A 662 1 16 HELIX 25 AC7 SER A 663 GLU A 665 5 3 HELIX 26 AC8 HIS A 666 ALA A 672 1 7 HELIX 27 AC9 GLU A 677 ARG A 693 1 17 HELIX 28 AD1 ARG A 693 SER A 701 1 9 HELIX 29 AD2 ALA A 715 GLN A 730 1 16 HELIX 30 AD3 GLU A 731 ARG A 740 1 10 HELIX 31 AD4 GLY A 755 ARG A 767 1 13 HELIX 32 AD5 VAL A 782 LEU A 791 1 10 HELIX 33 AD6 PRO A 792 GLY A 795 5 4 HELIX 34 AD7 SER A 808 LEU A 820 1 13 HELIX 35 AD8 THR A 836 GLY A 838 5 3 HELIX 36 AD9 CYS A 839 LYS A 850 1 12 HELIX 37 AE1 THR A 864 ASP A 877 1 14 HELIX 38 AE2 VAL A 891 SER A 904 1 14 HELIX 39 AE3 GLY A 920 ASN A 934 1 15 HELIX 40 AE4 LEU A 947 ARG A 961 1 15 HELIX 41 AE5 THR A 976 ASN A 990 1 15 HELIX 42 AE6 SER A 1004 ARG A 1014 1 11 SHEET 1 AA1 6 LEU A 237 VAL A 239 0 SHEET 2 AA1 6 VAL A 418 LEU A 424 -1 O ASN A 423 N GLU A 238 SHEET 3 AA1 6 THR A 274 VAL A 278 1 N LEU A 276 O PHE A 422 SHEET 4 AA1 6 ARG A 400 SER A 405 1 O LEU A 403 N VAL A 277 SHEET 5 AA1 6 ILE A 354 ASP A 359 1 N PHE A 358 O VAL A 402 SHEET 6 AA1 6 PHE A 307 SER A 312 1 N PHE A 309 O LEU A 355 SHEET 1 AA2 2 LEU A 565 VAL A 566 0 SHEET 2 AA2 2 GLU A 580 PHE A 581 -1 O GLU A 580 N VAL A 566 SHEET 1 AA311 HIS A 746 LYS A 748 0 SHEET 2 AA311 VAL A 773 GLN A 776 1 O GLN A 776 N LEU A 747 SHEET 3 AA311 CYS A 797 TYR A 801 1 O ALA A 799 N LEU A 775 SHEET 4 AA311 LYS A 827 ALA A 829 1 O ALA A 829 N LEU A 800 SHEET 5 AA311 ALA A 855 ARG A 857 1 O ARG A 857 N LEU A 828 SHEET 6 AA311 PHE A 883 GLY A 885 1 O PHE A 883 N LEU A 856 SHEET 7 AA311 TRP A 911 SER A 913 1 O SER A 913 N LEU A 884 SHEET 8 AA311 GLU A 939 CYS A 941 1 O CYS A 941 N LEU A 912 SHEET 9 AA311 VAL A 967 LYS A 969 1 O LYS A 969 N LEU A 940 SHEET 10 AA311 GLU A 995 TRP A 997 1 O TRP A 997 N LEU A 968 SHEET 11 AA311 LEU A1018 LEU A1019 1 O LEU A1019 N VAL A 996 CISPEP 1 GLU A 270 ASP A 271 0 8.45 CISPEP 2 ASP A 271 ALA A 272 0 13.86 CISPEP 3 GLY A 484 GLY A 485 0 5.55 SITE 1 AC1 18 ILE A 231 TYR A 232 THR A 233 GLU A 280 SITE 2 AC1 18 GLY A 282 SER A 283 GLY A 284 LYS A 285 SITE 3 AC1 18 SER A 286 THR A 287 PHE A 427 TYR A 435 SITE 4 AC1 18 PRO A 466 VAL A 467 TRP A 470 HIS A 583 SITE 5 AC1 18 HOH A1211 HOH A1237 CRYST1 77.815 106.162 185.393 90.00 90.00 90.00 P 21 21 21 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 0.012851 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009420 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005394 0.00000