HEADER TOXIN 07-AUG-07 2QV3 TITLE CRYSTAL STRUCTURE OF THE HELICOBACTER PYLORI VACUOLATING TOXIN P55 TITLE 2 DOMAIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: VACUOLATING CYTOTOXIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: P55; COMPND 5 SYNONYM: VACA; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 210; SOURCE 4 STRAIN: 60190; SOURCE 5 GENE: VACA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET41 KEYWDS BETA-HELIX, VACA, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR K.A.GANGWER REVDAT 5 25-OCT-17 2QV3 1 REMARK REVDAT 4 13-JUL-11 2QV3 1 VERSN REVDAT 3 24-FEB-09 2QV3 1 VERSN REVDAT 2 20-NOV-07 2QV3 1 JRNL REVDAT 1 23-OCT-07 2QV3 0 JRNL AUTH K.A.GANGWER,D.J.MUSHRUSH,D.L.STAUFF,B.SPILLER,M.S.MCCLAIN, JRNL AUTH 2 T.L.COVER,D.B.LACY JRNL TITL CRYSTAL STRUCTURE OF THE HELICOBACTER PYLORI VACUOLATING JRNL TITL 2 TOXIN P55 DOMAIN JRNL REF PROC.NATL.ACAD.SCI.USA V. 104 16293 2007 JRNL REFN ISSN 0027-8424 JRNL PMID 17911250 JRNL DOI 10.1073/PNAS.0707447104 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.03 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 19041 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) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.222 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 972 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1319 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 96.62 REMARK 3 BIN R VALUE (WORKING SET) : 0.1930 REMARK 3 BIN FREE R VALUE SET COUNT : 80 REMARK 3 BIN FREE R VALUE : 0.2570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3403 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 206 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.77 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.19000 REMARK 3 B22 (A**2) : -0.19000 REMARK 3 B33 (A**2) : 0.28000 REMARK 3 B12 (A**2) : -0.09000 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): 0.445 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.245 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.163 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 13.443 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 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): 3454 ; 0.023 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4679 ; 2.171 ; 1.932 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 445 ; 8.396 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 162 ;40.555 ;25.864 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 581 ;19.191 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;14.638 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 539 ; 0.168 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2615 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1398 ; 0.226 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2255 ; 0.317 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 246 ; 0.176 ; 0.200 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): 42 ; 0.239 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 7 ; 0.285 ; 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): 2263 ; 1.182 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3538 ; 1.927 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1354 ; 3.188 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1141 ; 4.919 ; 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 : 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 355 A 811 REMARK 3 ORIGIN FOR THE GROUP (A): 12.3801 37.0390 20.9406 REMARK 3 T TENSOR REMARK 3 T11: -0.0555 T22: -0.2030 REMARK 3 T33: -0.1325 T12: 0.0484 REMARK 3 T13: -0.0212 T23: 0.0479 REMARK 3 L TENSOR REMARK 3 L11: 1.1877 L22: 1.9862 REMARK 3 L33: 1.4772 L12: -0.5766 REMARK 3 L13: 0.0796 L23: -1.0713 REMARK 3 S TENSOR REMARK 3 S11: -0.0955 S12: -0.0423 S13: -0.1371 REMARK 3 S21: 0.0510 S22: 0.1046 S23: 0.2508 REMARK 3 S31: 0.0057 S32: -0.0171 S33: -0.0092 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 2QV3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-SEP-07. REMARK 100 THE DEPOSITION ID IS D_1000044092. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-JUL-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL SI-220 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 300 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19101 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.7 REMARK 200 DATA REDUNDANCY : 7.400 REMARK 200 R MERGE (I) : 0.06400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.49 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.7 REMARK 200 DATA REDUNDANCY IN SHELL : 7.60 REMARK 200 R MERGE FOR SHELL (I) : 0.41000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIRAS REMARK 200 SOFTWARE USED: SHARP, DM REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.41 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 18-23% PEG 1500, PH 8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 171.26333 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 85.63167 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 85.63167 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 171.26333 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 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 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 166 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 ASP A 367 REMARK 465 GLY A 368 REMARK 465 THR A 369 REMARK 465 ILE A 370 REMARK 465 LYS A 371 REMARK 465 VAL A 372 REMARK 465 GLY A 373 REMARK 465 GLY A 374 REMARK 465 PHE A 375 REMARK 465 LYS A 376 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 41 O HOH A 202 1.97 REMARK 500 O HOH A 119 O HOH A 121 2.13 REMARK 500 O HOH A 37 O HOH A 203 2.18 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 GLU A 548 CD GLU A 548 OE2 0.075 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 460 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 VAL A 509 CB - CA - C ANGL. DEV. = -11.8 DEGREES REMARK 500 LEU A 517 CB - CG - CD2 ANGL. DEV. = 13.5 DEGREES REMARK 500 GLY A 777 C - N - CA ANGL. DEV. = -13.0 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 383 149.00 -174.79 REMARK 500 SER A 396 -110.74 -106.12 REMARK 500 ASN A 397 -127.55 -105.32 REMARK 500 SER A 400 25.10 -144.23 REMARK 500 ARG A 402 75.98 -58.47 REMARK 500 THR A 403 129.49 84.24 REMARK 500 THR A 410 -45.76 -136.30 REMARK 500 TYR A 428 129.87 114.71 REMARK 500 ASN A 447 31.09 -140.73 REMARK 500 ASP A 455 150.04 -47.97 REMARK 500 LYS A 474 -103.62 -76.18 REMARK 500 ASN A 493 -70.72 -119.17 REMARK 500 ALA A 503 -70.77 -158.96 REMARK 500 LYS A 510 -61.77 -102.32 REMARK 500 SER A 553 -16.75 82.64 REMARK 500 SER A 563 160.74 176.90 REMARK 500 TRP A 577 31.39 70.97 REMARK 500 ARG A 592 -57.26 -140.36 REMARK 500 ASN A 611 -86.85 -82.98 REMARK 500 ASN A 658 -109.60 -129.64 REMARK 500 THR A 708 -26.87 -38.72 REMARK 500 ASN A 711 6.89 94.69 REMARK 500 ASN A 783 -167.73 -124.93 REMARK 500 ASN A 800 35.81 -97.41 REMARK 500 THR A 809 85.75 65.76 REMARK 500 ASN A 810 -93.38 -76.37 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 SER A 396 ASN A 397 -144.25 REMARK 500 ASN A 711 GLY A 712 -144.32 REMARK 500 GLY A 777 ILE A 778 134.59 REMARK 500 REMARK 500 REMARK: NULL DBREF 2QV3 A 355 811 UNP Q48245 VACA2_HELPY 388 844 SEQRES 1 A 457 THR VAL VAL ASN ILE ASP ARG ILE ASN THR LYS ALA ASP SEQRES 2 A 457 GLY THR ILE LYS VAL GLY GLY PHE LYS ALA SER LEU THR SEQRES 3 A 457 THR ASN ALA ALA HIS LEU ASN ILE GLY LYS GLY GLY VAL SEQRES 4 A 457 ASN LEU SER ASN GLN ALA SER GLY ARG THR LEU LEU VAL SEQRES 5 A 457 GLU ASN LEU THR GLY ASN ILE THR VAL ASP GLY PRO LEU SEQRES 6 A 457 ARG VAL ASN ASN GLN VAL GLY GLY TYR ALA LEU ALA GLY SEQRES 7 A 457 SER SER ALA ASN PHE GLU PHE LYS ALA GLY VAL ASP THR SEQRES 8 A 457 LYS ASN GLY THR ALA THR PHE ASN ASN ASP ILE SER LEU SEQRES 9 A 457 GLY ARG PHE VAL ASN LEU LYS VAL ASP ALA HIS THR ALA SEQRES 10 A 457 ASN PHE LYS GLY ILE ASP THR GLY ASN GLY GLY PHE ASN SEQRES 11 A 457 THR LEU ASP PHE SER GLY VAL THR ASN LYS VAL ASN ILE SEQRES 12 A 457 ASN LYS LEU ILE THR ALA SER THR ASN VAL ALA VAL LYS SEQRES 13 A 457 ASN PHE ASN ILE ASN GLU LEU ILE VAL LYS THR ASN GLY SEQRES 14 A 457 VAL SER VAL GLY GLU TYR THR HIS PHE SER GLU ASP ILE SEQRES 15 A 457 GLY SER GLN SER ARG ILE ASN THR VAL ARG LEU GLU THR SEQRES 16 A 457 GLY THR ARG SER ILE PHE SER GLY GLY VAL LYS PHE LYS SEQRES 17 A 457 SER GLY GLU LYS LEU VAL ILE ASP GLU PHE TYR TYR SER SEQRES 18 A 457 PRO TRP ASN TYR PHE ASP ALA ARG ASN ILE LYS ASN VAL SEQRES 19 A 457 GLU ILE THR ARG LYS PHE ALA SER SER THR PRO GLU ASN SEQRES 20 A 457 PRO TRP GLY THR SER LYS LEU MET PHE ASN ASN LEU THR SEQRES 21 A 457 LEU GLY GLN ASN ALA VAL MET ASP TYR SER GLN PHE SER SEQRES 22 A 457 ASN LEU THR ILE GLN GLY ASP PHE ILE ASN ASN GLN GLY SEQRES 23 A 457 THR ILE ASN TYR LEU VAL ARG GLY GLY LYS VAL ALA THR SEQRES 24 A 457 LEU ASN VAL GLY ASN ALA ALA ALA MET MET PHE ASN ASN SEQRES 25 A 457 ASP ILE ASP SER ALA THR GLY PHE TYR LYS PRO LEU ILE SEQRES 26 A 457 LYS ILE ASN SER ALA GLN ASP LEU ILE LYS ASN THR GLU SEQRES 27 A 457 HIS VAL LEU LEU LYS ALA LYS ILE ILE GLY TYR GLY ASN SEQRES 28 A 457 VAL SER THR GLY THR ASN GLY ILE SER ASN VAL ASN LEU SEQRES 29 A 457 GLU GLU GLN PHE LYS GLU ARG LEU ALA LEU TYR ASN ASN SEQRES 30 A 457 ASN ASN ARG MET ASP THR CYS VAL VAL ARG ASN THR ASP SEQRES 31 A 457 ASP ILE LYS ALA CYS GLY MET ALA ILE GLY ASN GLN SER SEQRES 32 A 457 MET VAL ASN ASN PRO ASP ASN TYR LYS TYR LEU ILE GLY SEQRES 33 A 457 LYS ALA TRP LYS ASN ILE GLY ILE SER LYS THR ALA ASN SEQRES 34 A 457 GLY SER LYS ILE SER VAL TYR TYR LEU GLY ASN SER THR SEQRES 35 A 457 PRO THR GLU ASN GLY GLY ASN THR THR ASN LEU PRO THR SEQRES 36 A 457 ASN THR FORMUL 2 HOH *206(H2 O) HELIX 1 1 SER A 683 LEU A 687 5 5 HELIX 2 2 ASN A 717 GLU A 724 1 8 HELIX 3 3 ASN A 742 GLY A 754 1 13 HELIX 4 4 ASN A 755 ASN A 761 1 7 HELIX 5 5 PRO A 762 ILE A 769 5 8 SHEET 1 A15 VAL A 357 ASN A 363 0 SHEET 2 A15 HIS A 385 LEU A 395 1 O ASN A 387 N VAL A 357 SHEET 3 A15 ASN A 412 VAL A 415 1 O THR A 414 N ILE A 388 SHEET 4 A15 THR A 449 PHE A 452 1 O THR A 451 N VAL A 415 SHEET 5 A15 VAL A 462 ASP A 477 1 O ASN A 472 N PHE A 452 SHEET 6 A15 ASN A 484 THR A 502 1 O LYS A 499 N ILE A 476 SHEET 7 A15 PHE A 512 VAL A 519 1 O ILE A 518 N LEU A 500 SHEET 8 A15 SER A 540 LEU A 547 1 O ARG A 546 N LEU A 517 SHEET 9 A15 VAL A 559 TYR A 574 1 O TYR A 573 N VAL A 545 SHEET 10 A15 TYR A 579 SER A 596 1 O ASP A 581 N VAL A 559 SHEET 11 A15 VAL A 620 TYR A 623 1 O ASP A 622 N PHE A 594 SHEET 12 A15 THR A 641 LEU A 645 1 O THR A 641 N MET A 621 SHEET 13 A15 ILE A 679 ASN A 682 1 O LYS A 680 N TYR A 644 SHEET 14 A15 LEU A 726 ASN A 730 1 O ALA A 727 N ILE A 679 SHEET 15 A15 ASN A 733 ARG A 734 -1 O ASN A 733 N ASN A 730 SHEET 1 B12 VAL A 357 ASN A 363 0 SHEET 2 B12 HIS A 385 LEU A 395 1 O ASN A 387 N VAL A 357 SHEET 3 B12 ASN A 412 VAL A 415 1 O THR A 414 N ILE A 388 SHEET 4 B12 THR A 449 PHE A 452 1 O THR A 451 N VAL A 415 SHEET 5 B12 VAL A 462 ASP A 477 1 O ASN A 472 N PHE A 452 SHEET 6 B12 ASN A 484 THR A 502 1 O LYS A 499 N ILE A 476 SHEET 7 B12 PHE A 512 VAL A 519 1 O ILE A 518 N LEU A 500 SHEET 8 B12 SER A 540 LEU A 547 1 O ARG A 546 N LEU A 517 SHEET 9 B12 VAL A 559 TYR A 574 1 O TYR A 573 N VAL A 545 SHEET 10 B12 TYR A 579 SER A 596 1 O ASP A 581 N VAL A 559 SHEET 11 B12 SER A 606 LEU A 615 1 O MET A 609 N ALA A 582 SHEET 12 B12 SER A 627 ILE A 631 1 O THR A 630 N LEU A 608 SHEET 1 C 3 VAL A 357 ASN A 363 0 SHEET 2 C 3 HIS A 385 LEU A 395 1 O ASN A 387 N VAL A 357 SHEET 3 C 3 LEU A 419 VAL A 421 1 O ARG A 420 N VAL A 393 SHEET 1 D 5 SER A 378 THR A 381 0 SHEET 2 D 5 LEU A 404 ASN A 408 1 O LEU A 405 N LEU A 379 SHEET 3 D 5 ALA A 435 ALA A 441 1 O GLU A 438 N VAL A 406 SHEET 4 D 5 VAL A 462 ASP A 477 1 O ASP A 467 N ALA A 441 SHEET 5 D 5 ILE A 456 SER A 457 1 N ILE A 456 O ASP A 477 SHEET 1 E 5 SER A 627 ILE A 631 0 SHEET 2 E 5 SER A 606 LEU A 615 1 N LEU A 608 O THR A 630 SHEET 3 E 5 PHE A 635 ASN A 638 1 O ILE A 636 N LEU A 615 SHEET 4 E 5 ALA A 659 PHE A 664 1 O ALA A 661 N ASN A 637 SHEET 5 E 5 ILE A 700 ASN A 705 1 O GLY A 702 N MET A 662 SHEET 1 F 7 THR A 530 ASP A 535 0 SHEET 2 F 7 THR A 505 ALA A 508 1 N THR A 505 O HIS A 531 SHEET 3 F 7 ASN A 484 THR A 502 1 N LEU A 486 O ASN A 506 SHEET 4 F 7 PHE A 512 VAL A 519 1 O ILE A 518 N LEU A 500 SHEET 5 F 7 SER A 540 LEU A 547 1 O ARG A 546 N LEU A 517 SHEET 6 F 7 VAL A 559 TYR A 574 1 O TYR A 573 N VAL A 545 SHEET 7 F 7 THR A 530 ASP A 535 1 N PHE A 532 O LYS A 562 SHEET 1 G 4 LEU A 654 ASN A 655 0 SHEET 2 G 4 GLU A 692 LYS A 697 1 O LEU A 695 N LEU A 654 SHEET 3 G 4 LYS A 786 TYR A 791 -1 O VAL A 789 N HIS A 693 SHEET 4 G 4 ILE A 778 ALA A 782 -1 N SER A 779 O TYR A 790 SHEET 1 H 3 THR A 737 VAL A 740 0 SHEET 2 H 3 LYS A 771 LYS A 774 -1 O TRP A 773 N CYS A 738 SHEET 3 H 3 THR A 804 ASN A 806 -1 O THR A 805 N ALA A 772 SSBOND 1 CYS A 738 CYS A 749 1555 1555 2.12 CRYST1 56.606 56.606 256.895 90.00 90.00 120.00 P 32 2 1 6 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 0.017666 0.010199 0.000000 0.00000 SCALE2 0.000000 0.020399 0.000000 0.00000 SCALE3 0.000000 0.000000 0.003893 0.00000