HEADER VIRAL PROTEIN 19-MAR-06 2GEC TITLE STRUCTURE OF THE N-TERMINAL DOMAIN OF AVIAN INFECTIOUS BRONCHITIS TITLE 2 VIRUS NUCLEOCAPSID PROTEIN (STRAIN GRAY) IN A NOVEL DIMERIC TITLE 3 ARRANGEMENT COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOCAPSID PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: N-TERMINAL DOMAIN; COMPND 5 SYNONYM: N STRUCTURAL PROTEIN, NC; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: INFECTIOUS BRONCHITIS VIRUS; SOURCE 3 ORGANISM_TAXID: 11120; SOURCE 4 STRAIN: GRAY; SOURCE 5 GENE: N; 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: PET 41 EK-LIC KEYWDS NUCLEOCAPSID PROTEIN, N PROTEIN, CORONAVIRUS, IBV N PROTEIN, VIRAL, KEYWDS 2 VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR H.JAYARAM,H.FAN,B.R.BOWMAN,A.OOI,J.JAYARAM,E.W.COLLISSON,J.LESCAR, AUTHOR 2 B.V.PRASAD REVDAT 3 30-AUG-23 2GEC 1 REMARK REVDAT 2 24-FEB-09 2GEC 1 VERSN REVDAT 1 27-JUN-06 2GEC 0 JRNL AUTH H.JAYARAM,H.FAN,B.R.BOWMAN,A.OOI,J.JAYARAM,E.W.COLLISSON, JRNL AUTH 2 J.LESCAR,B.V.PRASAD JRNL TITL X-RAY STRUCTURES OF THE N- AND C-TERMINAL DOMAINS OF A JRNL TITL 2 CORONAVIRUS NUCLEOCAPSID PROTEIN: IMPLICATIONS FOR JRNL TITL 3 NUCLEOCAPSID FORMATION. JRNL REF J.VIROL. V. 80 6612 2006 JRNL REFN ISSN 0022-538X JRNL PMID 16775348 JRNL DOI 10.1128/JVI.00157-06 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.42 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 89.5 REMARK 3 NUMBER OF REFLECTIONS : 60751 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.205 REMARK 3 FREE R VALUE : 0.246 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3256 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2856 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 58.09 REMARK 3 BIN R VALUE (WORKING SET) : 0.2810 REMARK 3 BIN FREE R VALUE SET COUNT : 187 REMARK 3 BIN FREE R VALUE : 0.3360 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2211 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 175 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.13000 REMARK 3 B22 (A**2) : 0.13000 REMARK 3 B33 (A**2) : -0.51000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.49000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.066 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.066 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.041 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.910 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.939 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.919 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2181 ; 0.026 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2960 ; 2.230 ; 1.924 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 261 ; 7.651 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 112 ;31.300 ;23.393 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 318 ;14.457 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 17 ;23.045 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 273 ; 0.148 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1777 ; 0.016 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 927 ; 0.239 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1477 ; 0.322 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 133 ; 0.290 ; 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): 60 ; 0.689 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 20 ; 0.936 ; 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): 1343 ; 3.358 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2108 ; 4.413 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 999 ; 6.060 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 852 ; 7.605 ; 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): 2342 ; 2.196 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 465 ; 3.255 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2118 ; 2.251 ; 3.000 REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : 1 REMARK 3 REMARK 3 NCS GROUP NUMBER : 1 REMARK 3 CHAIN NAMES : A B REMARK 3 NUMBER OF COMPONENTS NCS GROUP : 4 REMARK 3 COMPONENT C SSSEQI TO C SSSEQI CODE REMARK 3 1 A 25 A 50 4 REMARK 3 1 B 25 B 50 4 REMARK 3 2 A 51 A 76 4 REMARK 3 2 B 51 B 76 4 REMARK 3 3 A 77 A 87 4 REMARK 3 3 B 77 B 87 4 REMARK 3 4 A 88 A 150 4 REMARK 3 4 B 88 B 150 4 REMARK 3 GROUP CHAIN COUNT RMS WEIGHT REMARK 3 MEDIUM POSITIONAL 1 A (A): 862 ; 1.120 ; 0.500 REMARK 3 MEDIUM THERMAL 1 A (A**2): 862 ; 1.200 ; 2.000 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH 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 2GEC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 07-APR-06. REMARK 100 THE DEPOSITION ID IS D_1000037013. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-DEC-03 REMARK 200 TEMPERATURE (KELVIN) : 178 REMARK 200 PH : 6.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 14-BM-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9000 REMARK 200 MONOCHROMATOR : BENT CONICAL SI-MIRROR (RH REMARK 200 COATED) BENT GE(111) REMARK 200 MONOCHROMATOR REMARK 200 OPTICS : BENT CONICAL SI-MIRROR (RH REMARK 200 COATED) BENT GE(111) REMARK 200 MONOCHROMATOR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : ADSC REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 90638 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 87.9 REMARK 200 DATA REDUNDANCY : 3.300 REMARK 200 R MERGE (I) : 0.05600 REMARK 200 R SYM (I) : 0.05600 REMARK 200 FOR THE DATA SET : 49.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 REMARK 200 DATA REDUNDANCY IN SHELL : 3.30 REMARK 200 R MERGE FOR SHELL (I) : 0.22700 REMARK 200 R SYM FOR SHELL (I) : 0.22700 REMARK 200 FOR SHELL : 49.30 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ID 2BTL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.61 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.35 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25 % PEG 4000,100 MM MES SODIUM SALT, REMARK 280 PH 6.2, 200 MM MGCL2, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,Y+1/2,-Z REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 50.02750 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.10500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 50.02750 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 23.10500 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 300 REMARK: N-TERMINAL DOMAIN POSSIBLY DIMER IN SOLUTION. DIMER IN THE REMARK 300 ASSYMETRIC UNIT 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 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 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 163 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 PRO A 22 REMARK 475 REMARK 475 ZERO OCCUPANCY RESIDUES REMARK 475 THE FOLLOWING RESIDUES WERE MODELED WITH ZERO OCCUPANCY. REMARK 475 THE LOCATION AND PROPERTIES OF THESE RESIDUES MAY NOT REMARK 475 BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 475 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE) REMARK 475 M RES C SSEQI REMARK 475 GLY A 80 REMARK 475 LYS A 81 REMARK 475 GLY A 82 REMARK 475 ARG A 83 REMARK 475 ALA B 75 REMARK 475 ARG B 76 REMARK 475 PHE B 77 REMARK 475 LYS B 78 REMARK 475 PRO B 79 REMARK 475 GLY B 80 REMARK 475 LYS B 81 REMARK 475 GLY B 82 REMARK 475 ARG B 83 REMARK 475 ARG B 84 REMARK 475 LYS B 85 REMARK 475 PRO B 86 REMARK 475 VAL B 87 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 GLU B 52 CG CD OE1 OE2 REMARK 480 LYS B 63 CD CE NZ REMARK 480 GLN B 67 OE1 NE2 REMARK 480 GLN B 74 CD OE1 NE2 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 PRO A 79 N GLY A 80 1.69 REMARK 500 CA SER B 127 O HOH B 222 2.06 REMARK 500 N ASN B 128 O HOH B 209 2.18 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 CE LYS A 85 OD1 ASP B 135 1565 0.86 REMARK 500 NZ LYS A 85 OD1 ASP B 135 1565 1.29 REMARK 500 NZ LYS A 85 CG ASP B 135 1565 1.37 REMARK 500 NZ LYS A 85 OD2 ASP B 135 1565 1.48 REMARK 500 CD LYS A 85 OD1 ASP B 135 1565 1.95 REMARK 500 CE LYS A 85 CG ASP B 135 1565 2.01 REMARK 500 OD1 ASP B 103 O HOH A 216 3545 2.16 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 GLY A 80 C LYS A 81 N 0.170 REMARK 500 LYS A 81 C GLY A 82 N 0.230 REMARK 500 GLU B 60 CG GLU B 60 CD 0.091 REMARK 500 GLN B 74 CG GLN B 74 CD 0.377 REMARK 500 PRO B 86 C VAL B 87 N 0.272 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 23 NE - CZ - NH1 ANGL. DEV. = 7.6 DEGREES REMARK 500 ARG A 23 NE - CZ - NH2 ANGL. DEV. = -5.2 DEGREES REMARK 500 PRO A 79 CA - C - N ANGL. DEV. = 22.1 DEGREES REMARK 500 PRO A 79 O - C - N ANGL. DEV. = -40.7 DEGREES REMARK 500 ASP A 108 CB - CG - OD1 ANGL. DEV. = 5.9 DEGREES REMARK 500 ARG A 154 CG - CD - NE ANGL. DEV. = -13.5 DEGREES REMARK 500 ARG A 154 NE - CZ - NH1 ANGL. DEV. = 4.8 DEGREES REMARK 500 ARG A 154 NE - CZ - NH2 ANGL. DEV. = -3.9 DEGREES REMARK 500 ASP B 58 CB - CG - OD1 ANGL. DEV. = -6.6 DEGREES REMARK 500 TYR B 70 CZ - CE2 - CD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 GLN B 74 CB - CG - CD ANGL. DEV. = -24.8 DEGREES REMARK 500 ARG B 154 CD - NE - CZ ANGL. DEV. = 8.9 DEGREES REMARK 500 ARG B 154 NE - CZ - NH1 ANGL. DEV. = 10.2 DEGREES REMARK 500 ARG B 154 NE - CZ - NH2 ANGL. DEV. = -11.0 DEGREES REMARK 500 LEU B 160 CB - CA - C ANGL. DEV. = 11.5 DEGREES REMARK 500 LEU B 160 CA - CB - CG ANGL. DEV. = 17.4 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 ASN A 59 104.12 -166.00 REMARK 500 PRO A 79 -161.44 -72.06 REMARK 500 ARG A 83 108.66 31.61 REMARK 500 SER B 29 21.22 -68.63 REMARK 500 SER B 30 -145.13 28.59 REMARK 500 ASN B 59 103.03 -167.76 REMARK 500 ARG B 83 -91.32 151.87 REMARK 500 GLN B 110 130.78 -171.48 REMARK 500 VAL B 123 3.59 -69.76 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 PRO A 79 GLY A 80 -44.13 REMARK 500 GLY A 82 ARG A 83 47.98 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 PRO A 79 -40.74 REMARK 500 LYS A 81 -13.57 REMARK 500 ALA B 75 -10.90 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2BTL RELATED DB: PDB REMARK 900 N-PROTEIN STRUCTURE FROM AVIAN INFECTIOUS BRONCHITIS VIRUS (STRAIN REMARK 900 BEAUDETTE) PDB ID 2BTL IN A "SIDE-SIDE" DIMERIC ARRANGEMENT DBREF 2GEC A 22 160 UNP P32923 NCAP_IBVG 22 160 DBREF 2GEC B 22 160 UNP P32923 NCAP_IBVG 22 160 SEQADV 2GEC LEU A 62 UNP P32923 PHE 62 SEE REMARK 999 SEQADV 2GEC LEU B 62 UNP P32923 PHE 62 SEE REMARK 999 SEQRES 1 A 139 PRO ARG PRO PRO LYS VAL GLY SER SER GLY ASN ALA SER SEQRES 2 A 139 TRP PHE GLN ALA ILE LYS ALA LYS LYS LEU ASN SER PRO SEQRES 3 A 139 GLN PRO LYS PHE GLU GLY SER GLY VAL PRO ASP ASN GLU SEQRES 4 A 139 ASN LEU LYS THR SER GLN GLN HIS GLY TYR TRP ARG ARG SEQRES 5 A 139 GLN ALA ARG PHE LYS PRO GLY LYS GLY ARG ARG LYS PRO SEQRES 6 A 139 VAL PRO ASP ALA TRP TYR PHE TYR TYR THR GLY THR GLY SEQRES 7 A 139 PRO ALA ALA ASP LEU ASN TRP GLY ASP SER GLN ASP GLY SEQRES 8 A 139 ILE VAL TRP VAL ALA ALA LYS GLY ALA ASP VAL LYS SER SEQRES 9 A 139 ARG SER ASN GLN GLY THR ARG ASP PRO ASP LYS PHE ASP SEQRES 10 A 139 GLN TYR PRO LEU ARG PHE SER ASP GLY GLY PRO ASP GLY SEQRES 11 A 139 ASN PHE ARG TRP ASP PHE ILE PRO LEU SEQRES 1 B 139 PRO ARG PRO PRO LYS VAL GLY SER SER GLY ASN ALA SER SEQRES 2 B 139 TRP PHE GLN ALA ILE LYS ALA LYS LYS LEU ASN SER PRO SEQRES 3 B 139 GLN PRO LYS PHE GLU GLY SER GLY VAL PRO ASP ASN GLU SEQRES 4 B 139 ASN LEU LYS THR SER GLN GLN HIS GLY TYR TRP ARG ARG SEQRES 5 B 139 GLN ALA ARG PHE LYS PRO GLY LYS GLY ARG ARG LYS PRO SEQRES 6 B 139 VAL PRO ASP ALA TRP TYR PHE TYR TYR THR GLY THR GLY SEQRES 7 B 139 PRO ALA ALA ASP LEU ASN TRP GLY ASP SER GLN ASP GLY SEQRES 8 B 139 ILE VAL TRP VAL ALA ALA LYS GLY ALA ASP VAL LYS SER SEQRES 9 B 139 ARG SER ASN GLN GLY THR ARG ASP PRO ASP LYS PHE ASP SEQRES 10 B 139 GLN TYR PRO LEU ARG PHE SER ASP GLY GLY PRO ASP GLY SEQRES 11 B 139 ASN PHE ARG TRP ASP PHE ILE PRO LEU FORMUL 3 HOH *175(H2 O) HELIX 1 1 LYS A 63 GLN A 66 5 4 HELIX 2 2 LYS B 63 GLN B 66 5 4 SHEET 1 A 5 ILE A 113 ALA A 117 0 SHEET 2 A 5 HIS A 68 LYS A 78 -1 N GLY A 69 O VAL A 116 SHEET 3 A 5 LYS A 85 TYR A 95 -1 O ALA A 90 N GLN A 74 SHEET 4 A 5 ILE A 39 ALA A 41 -1 N ALA A 41 O ASP A 89 SHEET 5 A 5 PHE A 153 ARG A 154 -1 O ARG A 154 N LYS A 40 SHEET 1 B 5 ILE B 113 ALA B 117 0 SHEET 2 B 5 HIS B 68 LYS B 78 -1 N GLY B 69 O VAL B 116 SHEET 3 B 5 LYS B 85 TYR B 95 -1 O ALA B 90 N GLN B 74 SHEET 4 B 5 ILE B 39 ALA B 41 -1 N ALA B 41 O ASP B 89 SHEET 5 B 5 PHE B 153 ARG B 154 -1 O ARG B 154 N LYS B 40 CISPEP 1 GLY A 80 LYS A 81 0 12.98 CISPEP 2 LYS A 81 GLY A 82 0 -14.36 CRYST1 100.055 46.210 74.176 90.00 121.06 90.00 C 1 2 1 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 0.009995 0.000000 0.006020 0.00000 SCALE2 0.000000 0.021640 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015738 0.00000