HEADER LIGASE 10-MAY-07 2PVP TITLE CRYSTAL STRUCTURE OF D-ALANINE-D-ALANINE LIGASE FROM HELICOBACTER TITLE 2 PYLORI COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-ALANINE-D-ALANINE LIGASE; COMPND 3 CHAIN: A, B; COMPND 4 EC: 6.3.2.4; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI; SOURCE 3 ORGANISM_TAXID: 102617; SOURCE 4 STRAIN: SS1; SOURCE 5 GENE: DDL; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28B KEYWDS D-ALANINE-D-ALANINE LIGASE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR D.WU,L.ZHANG,H.JIANG,X.SHEN REVDAT 5 21-FEB-24 2PVP 1 SEQADV REVDAT 4 13-JUL-11 2PVP 1 VERSN REVDAT 3 24-FEB-09 2PVP 1 VERSN REVDAT 2 05-AUG-08 2PVP 1 JRNL REVDAT 1 01-APR-08 2PVP 0 JRNL AUTH D.WU,L.ZHANG,Y.KONG,J.DU,S.CHEN,J.CHEN,J.DING,H.JIANG,X.SHEN JRNL TITL ENZYMATIC CHARACTERIZATION AND CRYSTAL STRUCTURE ANALYSIS OF JRNL TITL 2 THE D-ALANINE-D-ALANINE LIGASE FROM HELICOBACTER PYLORI. JRNL REF PROTEINS V. 72 1148 2008 JRNL REFN ISSN 0887-3585 JRNL PMID 18320587 JRNL DOI 10.1002/PROT.22009 REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 97.5 REMARK 3 NUMBER OF REFLECTIONS : 30126 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.229 REMARK 3 FREE R VALUE : 0.283 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 1445 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5191 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 95 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 57.08 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : NULL ; NULL REMARK 3 ANGLE DISTANCE (A) : NULL ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2PVP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-MAY-07. REMARK 100 THE DEPOSITION ID IS D_1000042824. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-MAR-07 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 : PHOTON FACTORY REMARK 200 BEAMLINE : BL-17A 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 : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30126 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 122.169 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.06100 REMARK 200 R SYM (I) : 0.04400 REMARK 200 FOR THE DATA SET : 27.3000 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 (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 5.50 REMARK 200 R MERGE FOR SHELL (I) : 0.49100 REMARK 200 R SYM FOR SHELL (I) : 0.40300 REMARK 200 FOR SHELL : 2.880 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.36 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.29 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M HEPES, PH 7.5, 10% PEG6000, 5% REMARK 280 MPD, VAPOR DIFFUSION, HANGING 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 35.48450 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 60.94150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.50800 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 60.94150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 35.48450 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.50800 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 30450 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -15.8 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 LYS A 329 REMARK 465 THR A 330 REMARK 465 PRO A 331 REMARK 465 LYS A 332 REMARK 465 ILE A 333 REMARK 465 GLN A 334 REMARK 465 ILE A 335 REMARK 465 LYS A 336 REMARK 465 ASN A 337 REMARK 465 SER A 338 REMARK 465 TYR A 339 REMARK 465 LEU A 340 REMARK 465 LEU A 341 REMARK 465 GLN A 342 REMARK 465 ILE A 343 REMARK 465 GLN A 344 REMARK 465 LYS A 345 REMARK 465 ASN A 346 REMARK 465 LYS A 347 REMARK 465 MET B -19 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 GLU B 239 REMARK 465 PHE B 240 REMARK 465 LEU B 241 REMARK 465 ASP B 242 REMARK 465 PHE B 243 REMARK 465 LYS B 244 REMARK 465 GLN B 245 REMARK 465 LYS B 246 REMARK 465 TYR B 247 REMARK 465 LEU B 248 REMARK 465 ASP B 249 REMARK 465 PHE B 250 REMARK 465 SER B 251 REMARK 465 ARG B 252 REMARK 465 ASN B 253 REMARK 465 LYS B 254 REMARK 465 ALA B 255 REMARK 465 LYS B 332 REMARK 465 ILE B 333 REMARK 465 GLN B 334 REMARK 465 ILE B 335 REMARK 465 LYS B 336 REMARK 465 ASN B 337 REMARK 465 SER B 338 REMARK 465 TYR B 339 REMARK 465 LEU B 340 REMARK 465 LEU B 341 REMARK 465 GLN B 342 REMARK 465 ILE B 343 REMARK 465 GLN B 344 REMARK 465 LYS B 345 REMARK 465 ASN B 346 REMARK 465 LYS B 347 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 NZ LYS A 244 OG SER A 259 1.74 REMARK 500 CE1 TYR A 231 OD1 ASP A 242 1.81 REMARK 500 CD1 LEU B 179 O HOH B 386 1.97 REMARK 500 OE2 GLU A 239 O HOH A 376 2.04 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 OD1 ASP A 249 OG SER B 261 1655 1.93 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 VAL A 27 CB VAL A 27 CG1 0.283 REMARK 500 VAL A 27 CB VAL A 27 CG2 -0.366 REMARK 500 ILE A 32 CB ILE A 32 CG1 -0.314 REMARK 500 LYS A 225 CB LYS A 225 CG 0.278 REMARK 500 ASP A 226 CB ASP A 226 CG -0.132 REMARK 500 SER A 277 CB SER A 277 OG 0.341 REMARK 500 ASP A 278 CB ASP A 278 CG 0.193 REMARK 500 LEU A 279 CB LEU A 279 CG -0.376 REMARK 500 LYS B 29 CA LYS B 29 CB -0.214 REMARK 500 ASP B 30 CB ASP B 30 CG -0.278 REMARK 500 ARG B 31 CB ARG B 31 CG 0.304 REMARK 500 SER B 178 CB SER B 178 OG 0.198 REMARK 500 LYS B 225 CB LYS B 225 CG -0.334 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 VAL A 27 CA - CB - CG1 ANGL. DEV. = -19.2 DEGREES REMARK 500 VAL A 27 CA - CB - CG2 ANGL. DEV. = 17.4 DEGREES REMARK 500 ARG A 31 CB - CG - CD ANGL. DEV. = 32.9 DEGREES REMARK 500 ILE A 32 CA - CB - CG2 ANGL. DEV. = -13.8 DEGREES REMARK 500 ASP A 99 CB - CA - C ANGL. DEV. = -15.3 DEGREES REMARK 500 LYS A 225 CA - CB - CG ANGL. DEV. = -19.2 DEGREES REMARK 500 LYS A 257 O - C - N ANGL. DEV. = -11.0 DEGREES REMARK 500 LEU A 260 CB - CG - CD2 ANGL. DEV. = -20.8 DEGREES REMARK 500 TYR A 276 CB - CG - CD2 ANGL. DEV. = 19.7 DEGREES REMARK 500 TYR A 276 CB - CG - CD1 ANGL. DEV. = -24.6 DEGREES REMARK 500 ASP A 278 CA - CB - CG ANGL. DEV. = -15.6 DEGREES REMARK 500 ASP A 278 CB - CG - OD1 ANGL. DEV. = 14.8 DEGREES REMARK 500 ASP A 278 CB - CG - OD2 ANGL. DEV. = -11.4 DEGREES REMARK 500 LEU A 279 CA - CB - CG ANGL. DEV. = 17.4 DEGREES REMARK 500 VAL B 27 O - C - N ANGL. DEV. = 10.5 DEGREES REMARK 500 LEU B 28 CA - CB - CG ANGL. DEV. = -17.4 DEGREES REMARK 500 LEU B 28 CB - CG - CD1 ANGL. DEV. = -12.2 DEGREES REMARK 500 LEU B 28 CB - CG - CD2 ANGL. DEV. = 27.8 DEGREES REMARK 500 LYS B 29 CB - CA - C ANGL. DEV. = 13.2 DEGREES REMARK 500 ASP B 30 CA - CB - CG ANGL. DEV. = 28.9 DEGREES REMARK 500 ASP B 30 CB - CG - OD1 ANGL. DEV. = 19.5 DEGREES REMARK 500 ASP B 30 CB - CG - OD2 ANGL. DEV. = -18.4 DEGREES REMARK 500 ARG B 31 CA - CB - CG ANGL. DEV. = -15.1 DEGREES REMARK 500 LYS B 224 CB - CA - C ANGL. DEV. = 17.1 DEGREES REMARK 500 LYS B 225 CA - CB - CG ANGL. DEV. = 17.7 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 LYS A 29 -132.08 63.98 REMARK 500 HIS A 42 32.90 74.85 REMARK 500 LYS A 64 71.49 37.10 REMARK 500 ASN A 73 -0.33 70.79 REMARK 500 LEU A 90 117.94 -25.20 REMARK 500 ASP A 99 -21.29 75.26 REMARK 500 ARG A 120 -162.19 -79.54 REMARK 500 LYS A 153 31.36 -86.39 REMARK 500 ASN A 154 -17.37 -169.63 REMARK 500 ASN A 174 15.55 -156.45 REMARK 500 SER A 178 22.76 46.38 REMARK 500 GLU A 187 1.16 -64.44 REMARK 500 LYS A 224 -123.28 61.18 REMARK 500 TYR A 247 59.87 -97.99 REMARK 500 SER A 277 -99.04 5.60 REMARK 500 ASN A 294 -7.43 88.73 REMARK 500 LEU A 308 28.48 45.32 REMARK 500 TYR A 311 0.30 -68.27 REMARK 500 LYS B 29 -131.58 49.62 REMARK 500 HIS B 42 33.27 72.29 REMARK 500 LYS B 64 93.19 -37.97 REMARK 500 LEU B 90 114.24 -32.63 REMARK 500 ARG B 120 -168.54 -72.63 REMARK 500 LYS B 153 -79.58 -62.53 REMARK 500 ARG B 155 -70.89 -27.79 REMARK 500 ASN B 174 89.66 -159.65 REMARK 500 SER B 177 14.90 50.40 REMARK 500 LYS B 224 -141.38 68.73 REMARK 500 SER B 277 -129.16 31.25 REMARK 500 TYR B 311 0.61 -67.89 REMARK 500 THR B 330 88.60 -169.79 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 ASP A 30 ARG A 31 141.22 REMARK 500 LYS B 63 LYS B 64 -125.41 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 TYR A 276 0.13 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 2PVP A 1 347 UNP Q2N4T5 Q2N4T5_HELPY 1 347 DBREF 2PVP B 1 347 UNP Q2N4T5 Q2N4T5_HELPY 1 347 SEQADV 2PVP MET A -19 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP GLY A -18 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP SER A -17 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP SER A -16 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP HIS A -15 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP HIS A -14 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP HIS A -13 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP HIS A -12 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP HIS A -11 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP HIS A -10 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP SER A -9 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP SER A -8 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP GLY A -7 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP LEU A -6 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP VAL A -5 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP PRO A -4 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP ARG A -3 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP GLY A -2 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP SER A -1 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP HIS A 0 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP MET B -19 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP GLY B -18 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP SER B -17 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP SER B -16 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP HIS B -15 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP HIS B -14 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP HIS B -13 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP HIS B -12 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP HIS B -11 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP HIS B -10 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP SER B -9 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP SER B -8 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP GLY B -7 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP LEU B -6 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP VAL B -5 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP PRO B -4 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP ARG B -3 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP GLY B -2 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP SER B -1 UNP Q2N4T5 EXPRESSION TAG SEQADV 2PVP HIS B 0 UNP Q2N4T5 EXPRESSION TAG SEQRES 1 A 367 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 367 LEU VAL PRO ARG GLY SER HIS MET GLU PHE CYS VAL LEU SEQRES 3 A 367 PHE GLY GLY ALA SER PHE GLU HIS GLU ILE SER ILE VAL SEQRES 4 A 367 SER ALA ILE ALA LEU LYS GLY VAL LEU LYS ASP ARG ILE SEQRES 5 A 367 LYS TYR PHE ILE PHE LEU ASP GLU ASN HIS HIS PHE TYR SEQRES 6 A 367 LEU ILE GLU GLU SER ASN MET HIS SER LYS TYR PHE ALA SEQRES 7 A 367 GLN ILE LYS GLU LYS LYS LEU PRO PRO LEU ILE LEU THR SEQRES 8 A 367 HIS ASN GLY LEU LEU LYS ASN SER PHE LEU GLY ALA LYS SEQRES 9 A 367 ILE ILE GLU LEU PRO LEU VAL ILE ASN LEU VAL HIS GLY SEQRES 10 A 367 GLY ASP GLY GLU ASP GLY LYS LEU ALA SER LEU LEU GLU SEQRES 11 A 367 PHE TYR ARG ILE ALA PHE ILE GLY PRO ARG ILE GLU ALA SEQRES 12 A 367 SER VAL LEU SER TYR ASN LYS TYR LEU THR LYS LEU TYR SEQRES 13 A 367 ALA LYS ASP LEU GLY ILE LYS THR LEU ASP TYR VAL LEU SEQRES 14 A 367 LEU ASN GLU LYS ASN ARG ALA ASN ALA LEU ASP LEU MET SEQRES 15 A 367 ASN PHE ASN PHE PRO PHE ILE VAL LYS PRO SER ASN ALA SEQRES 16 A 367 GLY SER SER LEU GLY VAL ASN VAL VAL LYS GLU GLU LYS SEQRES 17 A 367 GLU LEU ILE TYR ALA LEU ASP SER ALA PHE GLU TYR SER SEQRES 18 A 367 LYS GLU VAL LEU ILE GLU PRO PHE ILE GLN GLY VAL LYS SEQRES 19 A 367 GLU TYR ASN LEU ALA GLY CYS LYS ILE LYS LYS ASP PHE SEQRES 20 A 367 CYS PHE SER TYR ILE GLU GLU PRO ASN LYS GLN GLU PHE SEQRES 21 A 367 LEU ASP PHE LYS GLN LYS TYR LEU ASP PHE SER ARG ASN SEQRES 22 A 367 LYS ALA PRO LYS ALA SER LEU SER ASN ALA LEU GLU GLU SEQRES 23 A 367 GLN LEU LYS GLU ASN PHE LYS LYS LEU TYR SER ASP LEU SEQRES 24 A 367 PHE ASP GLY ALA ILE ILE ARG CYS ASP PHE PHE VAL ILE SEQRES 25 A 367 GLU ASN GLU VAL TYR LEU ASN GLU ILE ASN PRO ILE PRO SEQRES 26 A 367 GLY SER LEU ALA ASN TYR LEU PHE ASP ASP PHE LYS THR SEQRES 27 A 367 THR LEU GLU ASN LEU ALA GLN SER LEU PRO LYS THR PRO SEQRES 28 A 367 LYS ILE GLN ILE LYS ASN SER TYR LEU LEU GLN ILE GLN SEQRES 29 A 367 LYS ASN LYS SEQRES 1 B 367 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 367 LEU VAL PRO ARG GLY SER HIS MET GLU PHE CYS VAL LEU SEQRES 3 B 367 PHE GLY GLY ALA SER PHE GLU HIS GLU ILE SER ILE VAL SEQRES 4 B 367 SER ALA ILE ALA LEU LYS GLY VAL LEU LYS ASP ARG ILE SEQRES 5 B 367 LYS TYR PHE ILE PHE LEU ASP GLU ASN HIS HIS PHE TYR SEQRES 6 B 367 LEU ILE GLU GLU SER ASN MET HIS SER LYS TYR PHE ALA SEQRES 7 B 367 GLN ILE LYS GLU LYS LYS LEU PRO PRO LEU ILE LEU THR SEQRES 8 B 367 HIS ASN GLY LEU LEU LYS ASN SER PHE LEU GLY ALA LYS SEQRES 9 B 367 ILE ILE GLU LEU PRO LEU VAL ILE ASN LEU VAL HIS GLY SEQRES 10 B 367 GLY ASP GLY GLU ASP GLY LYS LEU ALA SER LEU LEU GLU SEQRES 11 B 367 PHE TYR ARG ILE ALA PHE ILE GLY PRO ARG ILE GLU ALA SEQRES 12 B 367 SER VAL LEU SER TYR ASN LYS TYR LEU THR LYS LEU TYR SEQRES 13 B 367 ALA LYS ASP LEU GLY ILE LYS THR LEU ASP TYR VAL LEU SEQRES 14 B 367 LEU ASN GLU LYS ASN ARG ALA ASN ALA LEU ASP LEU MET SEQRES 15 B 367 ASN PHE ASN PHE PRO PHE ILE VAL LYS PRO SER ASN ALA SEQRES 16 B 367 GLY SER SER LEU GLY VAL ASN VAL VAL LYS GLU GLU LYS SEQRES 17 B 367 GLU LEU ILE TYR ALA LEU ASP SER ALA PHE GLU TYR SER SEQRES 18 B 367 LYS GLU VAL LEU ILE GLU PRO PHE ILE GLN GLY VAL LYS SEQRES 19 B 367 GLU TYR ASN LEU ALA GLY CYS LYS ILE LYS LYS ASP PHE SEQRES 20 B 367 CYS PHE SER TYR ILE GLU GLU PRO ASN LYS GLN GLU PHE SEQRES 21 B 367 LEU ASP PHE LYS GLN LYS TYR LEU ASP PHE SER ARG ASN SEQRES 22 B 367 LYS ALA PRO LYS ALA SER LEU SER ASN ALA LEU GLU GLU SEQRES 23 B 367 GLN LEU LYS GLU ASN PHE LYS LYS LEU TYR SER ASP LEU SEQRES 24 B 367 PHE ASP GLY ALA ILE ILE ARG CYS ASP PHE PHE VAL ILE SEQRES 25 B 367 GLU ASN GLU VAL TYR LEU ASN GLU ILE ASN PRO ILE PRO SEQRES 26 B 367 GLY SER LEU ALA ASN TYR LEU PHE ASP ASP PHE LYS THR SEQRES 27 B 367 THR LEU GLU ASN LEU ALA GLN SER LEU PRO LYS THR PRO SEQRES 28 B 367 LYS ILE GLN ILE LYS ASN SER TYR LEU LEU GLN ILE GLN SEQRES 29 B 367 LYS ASN LYS FORMUL 3 HOH *95(H2 O) HELIX 1 1 GLU A 13 LYS A 29 1 17 HELIX 2 2 GLU A 48 MET A 52 5 5 HELIX 3 3 HIS A 53 GLN A 59 1 7 HELIX 4 4 ILE A 60 LYS A 63 5 4 HELIX 5 5 GLY A 103 TYR A 112 1 10 HELIX 6 6 ARG A 120 ASN A 129 1 10 HELIX 7 7 ASN A 129 LEU A 140 1 12 HELIX 8 8 ASN A 154 ALA A 156 5 3 HELIX 9 9 ASN A 157 MET A 162 1 6 HELIX 10 10 GLU A 189 PHE A 198 1 10 HELIX 11 11 SER A 261 SER A 277 1 17 HELIX 12 12 PRO A 305 PHE A 313 5 9 HELIX 13 13 ASP A 315 LEU A 327 1 13 HELIX 14 14 GLU B 13 LYS B 29 1 17 HELIX 15 15 GLU B 48 MET B 52 5 5 HELIX 16 16 HIS B 53 GLN B 59 1 7 HELIX 17 17 ILE B 60 LYS B 64 5 5 HELIX 18 18 GLY B 97 ASP B 102 1 6 HELIX 19 19 GLY B 103 TYR B 112 1 10 HELIX 20 20 ARG B 120 ASN B 129 1 10 HELIX 21 21 ASN B 129 LEU B 140 1 12 HELIX 22 22 ASN B 154 ASP B 160 1 7 HELIX 23 23 GLU B 186 LYS B 188 5 3 HELIX 24 24 GLU B 189 GLU B 199 1 11 HELIX 25 25 SER B 261 SER B 277 1 17 HELIX 26 26 PRO B 305 PHE B 313 5 9 HELIX 27 27 ASP B 315 LEU B 327 1 13 SHEET 1 A 5 PHE A 44 LEU A 46 0 SHEET 2 A 5 ILE A 32 LEU A 38 -1 N PHE A 37 O TYR A 45 SHEET 3 A 5 PHE A 3 GLY A 8 1 N VAL A 5 O ILE A 36 SHEET 4 A 5 VAL A 91 ASN A 93 1 O ILE A 92 N CYS A 4 SHEET 5 A 5 PHE A 116 ILE A 117 1 O ILE A 117 N VAL A 91 SHEET 1 B 3 ILE A 69 THR A 71 0 SHEET 2 B 3 GLY A 74 SER A 79 -1 O LEU A 76 N ILE A 69 SHEET 3 B 3 GLY A 82 GLU A 87 -1 O LYS A 84 N LYS A 77 SHEET 1 C 4 VAL A 148 LEU A 150 0 SHEET 2 C 4 VAL A 204 PRO A 208 -1 O VAL A 204 N LEU A 150 SHEET 3 C 4 PHE A 168 PRO A 172 -1 N LYS A 171 O LEU A 205 SHEET 4 C 4 ASN A 182 VAL A 184 -1 O VAL A 184 N PHE A 168 SHEET 1 D 5 PHE A 240 LEU A 241 0 SHEET 2 D 5 ASP A 226 GLU A 233 -1 N ILE A 232 O LEU A 241 SHEET 3 D 5 LYS A 214 ILE A 223 -1 N ILE A 223 O ASP A 226 SHEET 4 D 5 ILE A 285 ILE A 292 -1 O PHE A 289 N TYR A 216 SHEET 5 D 5 GLU A 295 ASN A 302 -1 O ASN A 299 N ASP A 288 SHEET 1 E 5 PHE B 44 ILE B 47 0 SHEET 2 E 5 ILE B 32 LEU B 38 -1 N PHE B 35 O ILE B 47 SHEET 3 E 5 PHE B 3 GLY B 8 1 N PHE B 7 O LEU B 38 SHEET 4 E 5 VAL B 91 ASN B 93 1 O ILE B 92 N LEU B 6 SHEET 5 E 5 PHE B 116 ILE B 117 1 O ILE B 117 N ASN B 93 SHEET 1 F 3 ILE B 69 THR B 71 0 SHEET 2 F 3 GLY B 74 SER B 79 -1 O GLY B 74 N THR B 71 SHEET 3 F 3 GLY B 82 GLU B 87 -1 O LYS B 84 N LYS B 77 SHEET 1 G 4 VAL B 148 ASN B 151 0 SHEET 2 G 4 GLU B 203 PRO B 208 -1 O VAL B 204 N LEU B 150 SHEET 3 G 4 PHE B 168 PRO B 172 -1 N LYS B 171 O LEU B 205 SHEET 4 G 4 ASN B 182 VAL B 184 -1 O VAL B 184 N PHE B 168 SHEET 1 H 4 ASP B 226 PHE B 229 0 SHEET 2 H 4 LYS B 214 ILE B 223 -1 N ILE B 223 O ASP B 226 SHEET 3 H 4 ILE B 285 ILE B 292 -1 O PHE B 289 N TYR B 216 SHEET 4 H 4 GLU B 295 ASN B 302 -1 O ASN B 302 N ARG B 286 CISPEP 1 PHE A 166 PRO A 167 0 4.48 CISPEP 2 PHE B 166 PRO B 167 0 -6.63 CRYST1 70.969 89.016 121.883 90.00 90.00 90.00 P 21 21 21 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 0.014091 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011234 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008205 0.00000