HEADER HYDROLASE 12-JAN-10 3LD1 TITLE CRYSTAL STRUCTURE OF IBV NSP2A COMPND MOL_ID: 1; COMPND 2 MOLECULE: REPLICASE POLYPROTEIN 1A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: IBV NSP2A; COMPND 5 SYNONYM: PP1A, ORF1A POLYPROTEIN, NON-STRUCTURAL PROTEIN 2, NSP2, COMPND 6 P87, NON-STRUCTURAL PROTEIN 3, NSP3, PAPAIN-LIKE PROTEINASE, PL-PRO, COMPND 7 P195, NON-STRUCTURAL PROTEIN 4, NSP4, PEPTIDE HD2, P41, 3C-LIKE COMPND 8 PROTEINASE, 3CL-PRO, 3CLP, M-PRO, P33, NSP5, NON-STRUCTURAL PROTEIN COMPND 9 6, NSP6, P34, NON-STRUCTURAL PROTEIN 7, NSP7, P9, NON-STRUCTURAL COMPND 10 PROTEIN 8, NSP8, P24, NON-STRUCTURAL PROTEIN 9, NSP9, P10, NON- COMPND 11 STRUCTURAL PROTEIN 10, NSP10, GROWTH FACTOR-LIKE PEPTIDE, GFL, P16, COMPND 12 NON-STRUCTURAL PROTEIN 11, NSP11; COMPND 13 EC: 3.4.22.-; COMPND 14 ENGINEERED: YES; COMPND 15 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: AVIAN INFECTIOUS BRONCHITIS VIRUS (STRAIN M41); SOURCE 3 ORGANISM_COMMON: IBV; SOURCE 4 ORGANISM_TAXID: 11127; SOURCE 5 STRAIN: M41; SOURCE 6 GENE: 1A, 1AB; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PGEX-6P-1 KEYWDS GLOBULAR LIKE, HOST CYTOPLASM, HOST MEMBRANE, MEMBRANE, METAL- KEYWDS 2 BINDING, PROTEASE, RNA-BINDING, THIOL PROTEASE, TRANSMEMBRANE, ZINC- KEYWDS 3 FINGER, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.XU,L.CONG,L.WEI,J.FU,C.CHEN,A.YANG,H.TANG,M.BARTLAM,Z.RAO REVDAT 4 21-FEB-24 3LD1 1 REMARK REVDAT 3 13-OCT-21 3LD1 1 SEQADV REVDAT 2 01-NOV-17 3LD1 1 REMARK REVDAT 1 25-MAY-11 3LD1 0 JRNL AUTH Y.XU,Z.YE,L.WEI,L.CONG,J.FU,C.CHEN,A.YANG,W.WU,H.TANG, JRNL AUTH 2 M.BARTLAM,Z.RAO JRNL TITL IBV NSP2 IS AN ENDOSOME-ASSOCIATED PROTEIN AND VIRAL JRNL TITL 2 PATHOGENICITY FACTOR JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.50 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.14 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 15851 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) : 0.219 REMARK 3 R VALUE (WORKING SET) : 0.216 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 792 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1097 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.05 REMARK 3 BIN R VALUE (WORKING SET) : 0.2700 REMARK 3 BIN FREE R VALUE SET COUNT : 59 REMARK 3 BIN FREE R VALUE : 0.4700 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2792 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 90 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 51.98 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.17000 REMARK 3 B22 (A**2) : -2.17000 REMARK 3 B33 (A**2) : 3.25000 REMARK 3 B12 (A**2) : -1.08000 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): 0.488 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.308 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.230 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 10.177 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.943 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.913 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2845 ; 0.026 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3845 ; 2.217 ; 1.961 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 358 ; 7.982 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 120 ;37.291 ;23.750 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 501 ;21.810 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;20.979 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 446 ; 0.139 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2105 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1387 ; 0.281 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1983 ; 0.331 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 150 ; 0.179 ; 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): 22 ; 0.190 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 2 ; 0.207 ; 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): 1836 ; 1.258 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2873 ; 2.106 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1148 ; 3.025 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 972 ; 4.517 ; 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 : NULL 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 3LD1 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JAN-10. REMARK 100 THE DEPOSITION ID IS D_1000057126. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-OCT-08 REMARK 200 TEMPERATURE (KELVIN) : NULL 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-5A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9798 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MONOCHROMATER REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO, HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17086 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.490 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 200 DATA REDUNDANCY : 13.80 REMARK 200 R MERGE (I) : 0.07500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 30.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.49 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.2 REMARK 200 DATA REDUNDANCY IN SHELL : 11.60 REMARK 200 R MERGE FOR SHELL (I) : 0.39000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: SOLVE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.38 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.89 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12% (W/V) PEG8000, 10% (V/V) ETHYLENE REMARK 280 GLYCOL, 100MM HEPES, PH 7.5, VAPOR DIFFUSION, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,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 20.32633 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 40.65267 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 20.32633 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 40.65267 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 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 LYS A 70 CD LYS A 70 CE 0.156 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 CYS A 20 CA - CB - SG ANGL. DEV. = -14.1 DEGREES REMARK 500 ASP A 36 CB - CG - OD1 ANGL. DEV. = 5.4 DEGREES REMARK 500 LEU A 136 CB - CG - CD1 ANGL. DEV. = 11.0 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 ASP A 33 -163.29 -163.37 REMARK 500 GLU A 57 101.31 -59.23 REMARK 500 ASP A 69 -110.15 -113.82 REMARK 500 THR A 72 127.43 -38.88 REMARK 500 VAL A 75 73.13 -33.99 REMARK 500 ASN A 169 -30.89 -27.59 REMARK 500 PHE A 174 -49.77 -22.13 REMARK 500 GLN A 175 1.08 -43.51 REMARK 500 ILE A 176 5.91 -64.45 REMARK 500 PHE A 177 -86.15 -42.95 REMARK 500 GLN A 179 31.24 -78.09 REMARK 500 GLN A 180 -154.09 -141.19 REMARK 500 ILE A 181 -70.03 -3.98 REMARK 500 ASN A 194 86.71 -10.18 REMARK 500 SER A 196 -27.03 67.49 REMARK 500 THR A 260 -141.36 63.78 REMARK 500 GLN A 311 131.23 177.06 REMARK 500 GLU A 314 62.57 62.71 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 GLN A 175 ILE A 176 149.89 REMARK 500 GLN A 179 GLN A 180 -149.44 REMARK 500 REMARK 500 REMARK: NULL DBREF 3LD1 A 5 363 UNP P0C6V5 R1A_IBVM 13 371 SEQADV 3LD1 LEU A 124 UNP P0C6V5 GLN 132 ENGINEERED MUTATION SEQADV 3LD1 ALA A 187 UNP P0C6V5 LYS 195 ENGINEERED MUTATION SEQADV 3LD1 PHE A 262 UNP P0C6V5 LEU 270 ENGINEERED MUTATION SEQRES 1 A 359 LEU ARG ASP VAL ILE LEU VAL SER LYS ASP ILE PRO GLU SEQRES 2 A 359 GLN LEU CYS ASP ALA LEU PHE PHE TYR THR SER HIS ASN SEQRES 3 A 359 PRO LYS ASP TYR ALA ASP ALA PHE ALA VAL ARG GLN LYS SEQRES 4 A 359 PHE ASP ARG ASN LEU GLN THR GLY LYS GLN PHE LYS PHE SEQRES 5 A 359 GLU THR VAL CYS GLY LEU PHE LEU LEU LYS GLY VAL ASP SEQRES 6 A 359 LYS ILE THR PRO GLY VAL PRO ALA LYS VAL LEU LYS ALA SEQRES 7 A 359 THR SER LYS LEU ALA ASP LEU GLU ASP ILE PHE GLY VAL SEQRES 8 A 359 SER PRO PHE ALA ARG LYS TYR ARG GLU LEU LEU LYS THR SEQRES 9 A 359 ALA CYS GLN TRP SER LEU THR VAL GLU THR LEU ASP ALA SEQRES 10 A 359 ARG ALA LEU THR LEU ASP GLU ILE PHE ASP PRO THR GLU SEQRES 11 A 359 ILE LEU TRP LEU GLN VAL ALA ALA LYS ILE GLN VAL SER SEQRES 12 A 359 ALA MET ALA MET ARG ARG LEU VAL GLY GLU VAL THR ALA SEQRES 13 A 359 LYS VAL MET ASP ALA LEU GLY SER ASN MET SER ALA LEU SEQRES 14 A 359 PHE GLN ILE PHE LYS GLN GLN ILE VAL ARG ILE PHE GLN SEQRES 15 A 359 ALA ALA LEU ALA ILE PHE GLU ASN VAL SER GLU LEU PRO SEQRES 16 A 359 GLN ARG ILE ALA ALA LEU LYS MET ALA PHE ALA LYS CYS SEQRES 17 A 359 ALA LYS SER ILE THR VAL VAL VAL MET GLU ARG THR LEU SEQRES 18 A 359 VAL VAL ARG GLU PHE ALA GLY THR CYS LEU ALA SER ILE SEQRES 19 A 359 ASN GLY ALA VAL ALA LYS PHE PHE GLU GLU LEU PRO ASN SEQRES 20 A 359 GLY PHE MET GLY ALA LYS ILE PHE THR THR PHE ALA PHE SEQRES 21 A 359 PHE ARG GLU ALA ALA VAL LYS ILE VAL ASP ASN ILE PRO SEQRES 22 A 359 ASN ALA PRO ARG GLY THR LYS GLY PHE GLU VAL VAL GLY SEQRES 23 A 359 ASN ALA LYS GLY THR GLN VAL VAL VAL ARG GLY MET ARG SEQRES 24 A 359 ASN ASP LEU THR LEU LEU ASP GLN LYS ALA GLU ILE PRO SEQRES 25 A 359 VAL GLU SER GLU GLY TRP SER ALA ILE LEU GLY GLY HIS SEQRES 26 A 359 LEU CYS TYR VAL PHE LYS SER GLY ASP ARG PHE TYR ALA SEQRES 27 A 359 ALA PRO LEU SER GLY ASN PHE ALA LEU HIS ASP VAL HIS SEQRES 28 A 359 CYS CYS GLU ARG VAL VAL CYS LEU FORMUL 2 HOH *90(H2 O) HELIX 1 1 PRO A 16 PHE A 25 1 10 HELIX 2 2 ASP A 33 GLY A 51 1 19 HELIX 3 3 LYS A 85 GLY A 94 1 10 HELIX 4 4 SER A 96 THR A 108 1 13 HELIX 5 5 THR A 108 SER A 113 1 6 HELIX 6 6 THR A 115 LEU A 126 1 12 HELIX 7 7 ASP A 127 ILE A 129 5 3 HELIX 8 8 ASP A 131 GLN A 139 1 9 HELIX 9 9 LYS A 143 GLY A 167 1 25 HELIX 10 10 MET A 170 GLN A 175 1 6 HELIX 11 11 GLN A 180 ALA A 190 1 11 HELIX 12 12 GLU A 197 CYS A 212 1 16 HELIX 13 13 GLU A 229 ALA A 231 5 3 HELIX 14 14 LEU A 235 GLU A 248 1 14 HELIX 15 15 GLY A 252 ALA A 256 5 5 SHEET 1 A 4 PHE A 54 THR A 58 0 SHEET 2 A 4 GLY A 61 VAL A 68 -1 O PHE A 63 N PHE A 56 SHEET 3 A 4 VAL A 8 SER A 12 1 N ILE A 9 O LEU A 64 SHEET 4 A 4 LYS A 78 LEU A 80 1 O LYS A 78 N LEU A 10 SHEET 1 B 2 VAL A 218 MET A 221 0 SHEET 2 B 2 THR A 224 VAL A 227 -1 O THR A 224 N MET A 221 SHEET 1 C 4 LYS A 257 PHE A 259 0 SHEET 2 C 4 PHE A 262 PHE A 264 -1 O PHE A 262 N PHE A 259 SHEET 3 C 4 ALA A 269 VAL A 273 -1 O VAL A 270 N ALA A 263 SHEET 4 C 4 GLY A 285 VAL A 289 -1 O VAL A 289 N ALA A 269 SHEET 1 D 6 THR A 295 GLN A 296 0 SHEET 2 D 6 PHE A 349 ALA A 350 -1 O ALA A 350 N THR A 295 SHEET 3 D 6 ARG A 339 SER A 346 -1 N SER A 346 O PHE A 349 SHEET 4 D 6 HIS A 329 SER A 336 -1 N TYR A 332 O ALA A 343 SHEET 5 D 6 GLU A 320 LEU A 326 -1 N LEU A 326 O HIS A 329 SHEET 6 D 6 VAL A 298 MET A 302 1 N ARG A 300 O GLY A 321 SHEET 1 E 5 THR A 295 GLN A 296 0 SHEET 2 E 5 PHE A 349 ALA A 350 -1 O ALA A 350 N THR A 295 SHEET 3 E 5 ARG A 339 SER A 346 -1 N SER A 346 O PHE A 349 SHEET 4 E 5 HIS A 355 ARG A 359 -1 O HIS A 355 N ALA A 342 SHEET 5 E 5 LEU A 306 LYS A 312 -1 N GLN A 311 O CYS A 356 CRYST1 114.179 114.179 60.979 90.00 90.00 120.00 P 64 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 0.008758 0.005057 0.000000 0.00000 SCALE2 0.000000 0.010113 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016399 0.00000