HEADER VIRAL PROTEIN 23-JAN-20 6XW5 TITLE CRYSTAL STRUCTURE OF MURINE NOROVIRUS P DOMAIN IN COMPLEX WITH TITLE 2 NANOBODY NB-5820 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CAPSID PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: NANOBODY NB-5820; COMPND 7 CHAIN: C, D; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MURINE NOROVIRUS 1; SOURCE 3 ORGANISM_TAXID: 223997; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PMALC2X; SOURCE 7 MOL_ID: 2; SOURCE 8 ORGANISM_SCIENTIFIC: VICUGNA PACOS; SOURCE 9 ORGANISM_TAXID: 30538; SOURCE 10 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 11 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 12 EXPRESSION_SYSTEM_STRAIN: WK6; SOURCE 13 EXPRESSION_SYSTEM_PLASMID: PHEN6C KEYWDS MNV, NEUTRALIZING NANOBODY, VHH, NOROVIRUS, VIRAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.KILIC,C.SABIN,G.HANSMAN REVDAT 4 24-JAN-24 6XW5 1 REMARK REVDAT 3 01-JUL-20 6XW5 1 JRNL REVDAT 2 06-MAY-20 6XW5 1 JRNL REVDAT 1 22-APR-20 6XW5 0 JRNL AUTH A.D.KOROMYSLOVA,J.M.DEVANT,T.KILIC,C.D.SABIN,V.MALAK, JRNL AUTH 2 G.S.HANSMAN JRNL TITL NANOBODY-MEDIATED NEUTRALIZATION REVEALS AN ACHILLES HEEL JRNL TITL 2 FOR NOROVIRUS. JRNL REF J.VIROL. V. 94 2020 JRNL REFN ESSN 1098-5514 JRNL PMID 32321816 JRNL DOI 10.1128/JVI.00660-20 REMARK 2 REMARK 2 RESOLUTION. 1.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 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) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.86 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 121577 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) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.191 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 6299 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.72 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.76 REMARK 3 REFLECTION IN BIN (WORKING SET) : 8781 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE SET COUNT : 447 REMARK 3 BIN FREE R VALUE : 0.2720 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6484 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 44 REMARK 3 SOLVENT ATOMS : 712 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 30.81 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.63 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.08000 REMARK 3 B22 (A**2) : 1.08000 REMARK 3 B33 (A**2) : -2.17000 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): 0.080 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.082 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.057 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.784 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.971 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.962 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6795 ; 0.012 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 6165 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9266 ; 1.735 ; 1.649 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14279 ; 1.464 ; 1.567 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 868 ; 7.610 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 341 ;31.586 ;21.525 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1020 ;12.074 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 48 ;20.136 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 877 ; 0.080 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7757 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1499 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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 : 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6XW5 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 23-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1292106287. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-JUL-18 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 : ESRF REMARK 200 BEAMLINE : ID29 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.072270 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 127876 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.720 REMARK 200 RESOLUTION RANGE LOW (A) : 49.860 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 13.01 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.3400 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.76 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 12.46 REMARK 200 R MERGE FOR SHELL (I) : 0.79100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.040 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: 3LQ6 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 25% PEG3000, 0.1M TRIS PH 8.5, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 114.26000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 50.86000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 50.86000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 57.13000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 50.86000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 50.86000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 171.39000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 50.86000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 50.86000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 57.13000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 50.86000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 50.86000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 171.39000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 114.26000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 10700 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 10.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D 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 847 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 LEU A 533 REMARK 465 HIS C 118 REMARK 465 HIS C 119 REMARK 465 HIS C 120 REMARK 465 HIS C 121 REMARK 465 HIS C 122 REMARK 465 HIS C 123 REMARK 465 HIS D 121 REMARK 465 HIS D 122 REMARK 465 HIS D 123 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 MET D 77 CA CB CG SD CE 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 B 478 NE - CZ - NH1 ANGL. DEV. = 4.2 DEGREES REMARK 500 ARG B 478 NE - CZ - NH2 ANGL. DEV. = -3.4 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 GLN A 263 47.53 -107.96 REMARK 500 THR A 301 -63.15 -128.32 REMARK 500 ASN A 364 69.30 -116.30 REMARK 500 ALA A 368 58.90 -146.68 REMARK 500 ASN A 409 48.04 -157.38 REMARK 500 SER A 470 -157.35 -155.61 REMARK 500 LEU A 481 -70.53 -68.61 REMARK 500 SER B 299 123.10 -36.33 REMARK 500 PRO B 361 45.67 -77.39 REMARK 500 ALA B 368 65.12 -159.27 REMARK 500 THR B 441 -75.22 31.28 REMARK 500 ASP B 512 44.23 -102.44 REMARK 500 THR C 32 -93.46 -112.79 REMARK 500 THR D 32 -96.18 -99.99 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 EDO A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue TRS A 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 603 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 604 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 700 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO C 701 DBREF 6XW5 A 228 533 UNP Q80J94 Q80J94_9CALI 228 533 DBREF 6XW5 B 228 533 UNP Q80J94 Q80J94_9CALI 228 533 DBREF 6XW5 C 1 123 PDB 6XW5 6XW5 1 123 DBREF 6XW5 D 1 123 PDB 6XW5 6XW5 1 123 SEQRES 1 A 306 ARG MET VAL ASP LEU PRO VAL ILE GLN PRO ARG LEU CYS SEQRES 2 A 306 THR HIS ALA ARG TRP PRO ALA PRO VAL TYR GLY LEU LEU SEQRES 3 A 306 VAL ASP PRO SER LEU PRO SER ASN PRO GLN TRP GLN ASN SEQRES 4 A 306 GLY ARG VAL HIS VAL ASP GLY THR LEU LEU GLY THR THR SEQRES 5 A 306 PRO ILE SER GLY SER TRP VAL SER CYS PHE ALA ALA GLU SEQRES 6 A 306 ALA ALA TYR LYS PHE GLN SER GLY THR GLY GLU VAL ALA SEQRES 7 A 306 THR PHE THR LEU ILE GLU GLN ASP GLY SER ALA TYR VAL SEQRES 8 A 306 PRO GLY ASP ARG ALA ALA PRO LEU GLY TYR PRO ASP PHE SEQRES 9 A 306 SER GLY GLN LEU GLU ILE GLU VAL GLN THR GLU THR THR SEQRES 10 A 306 LYS THR GLY ASP LYS LEU LYS VAL THR THR PHE GLU MET SEQRES 11 A 306 ILE LEU GLY PRO THR THR ASN ALA ASP GLN ALA PRO TYR SEQRES 12 A 306 GLN GLY ARG VAL PHE ALA SER VAL THR ALA ALA ALA SER SEQRES 13 A 306 LEU ASP LEU VAL ASP GLY ARG VAL ARG ALA VAL PRO ARG SEQRES 14 A 306 SER ILE TYR GLY PHE GLN ASP THR ILE PRO GLU TYR ASN SEQRES 15 A 306 ASP GLY LEU LEU VAL PRO LEU ALA PRO PRO ILE GLY PRO SEQRES 16 A 306 PHE LEU PRO GLY GLU VAL LEU LEU ARG PHE ARG THR TYR SEQRES 17 A 306 MET ARG GLN ILE ASP THR ALA ASP ALA ALA ALA GLU ALA SEQRES 18 A 306 ILE ASP CYS ALA LEU PRO GLN GLU PHE VAL SER TRP PHE SEQRES 19 A 306 ALA SER ASN ALA PHE THR VAL GLN SER GLU ALA LEU LEU SEQRES 20 A 306 LEU ARG TYR ARG ASN THR LEU THR GLY GLN LEU LEU PHE SEQRES 21 A 306 GLU CYS LYS LEU TYR ASN GLU GLY TYR ILE ALA LEU SER SEQRES 22 A 306 TYR SER GLY SER GLY PRO LEU THR PHE PRO THR ASP GLY SEQRES 23 A 306 ILE PHE GLU VAL VAL SER TRP VAL PRO ARG LEU TYR GLN SEQRES 24 A 306 LEU ALA SER VAL GLY SER LEU SEQRES 1 B 306 ARG MET VAL ASP LEU PRO VAL ILE GLN PRO ARG LEU CYS SEQRES 2 B 306 THR HIS ALA ARG TRP PRO ALA PRO VAL TYR GLY LEU LEU SEQRES 3 B 306 VAL ASP PRO SER LEU PRO SER ASN PRO GLN TRP GLN ASN SEQRES 4 B 306 GLY ARG VAL HIS VAL ASP GLY THR LEU LEU GLY THR THR SEQRES 5 B 306 PRO ILE SER GLY SER TRP VAL SER CYS PHE ALA ALA GLU SEQRES 6 B 306 ALA ALA TYR LYS PHE GLN SER GLY THR GLY GLU VAL ALA SEQRES 7 B 306 THR PHE THR LEU ILE GLU GLN ASP GLY SER ALA TYR VAL SEQRES 8 B 306 PRO GLY ASP ARG ALA ALA PRO LEU GLY TYR PRO ASP PHE SEQRES 9 B 306 SER GLY GLN LEU GLU ILE GLU VAL GLN THR GLU THR THR SEQRES 10 B 306 LYS THR GLY ASP LYS LEU LYS VAL THR THR PHE GLU MET SEQRES 11 B 306 ILE LEU GLY PRO THR THR ASN ALA ASP GLN ALA PRO TYR SEQRES 12 B 306 GLN GLY ARG VAL PHE ALA SER VAL THR ALA ALA ALA SER SEQRES 13 B 306 LEU ASP LEU VAL ASP GLY ARG VAL ARG ALA VAL PRO ARG SEQRES 14 B 306 SER ILE TYR GLY PHE GLN ASP THR ILE PRO GLU TYR ASN SEQRES 15 B 306 ASP GLY LEU LEU VAL PRO LEU ALA PRO PRO ILE GLY PRO SEQRES 16 B 306 PHE LEU PRO GLY GLU VAL LEU LEU ARG PHE ARG THR TYR SEQRES 17 B 306 MET ARG GLN ILE ASP THR ALA ASP ALA ALA ALA GLU ALA SEQRES 18 B 306 ILE ASP CYS ALA LEU PRO GLN GLU PHE VAL SER TRP PHE SEQRES 19 B 306 ALA SER ASN ALA PHE THR VAL GLN SER GLU ALA LEU LEU SEQRES 20 B 306 LEU ARG TYR ARG ASN THR LEU THR GLY GLN LEU LEU PHE SEQRES 21 B 306 GLU CYS LYS LEU TYR ASN GLU GLY TYR ILE ALA LEU SER SEQRES 22 B 306 TYR SER GLY SER GLY PRO LEU THR PHE PRO THR ASP GLY SEQRES 23 B 306 ILE PHE GLU VAL VAL SER TRP VAL PRO ARG LEU TYR GLN SEQRES 24 B 306 LEU ALA SER VAL GLY SER LEU SEQRES 1 C 123 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 C 123 ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 C 123 ARG THR PHE SER LEU THR THR MET GLY TRP PHE ARG GLN SEQRES 4 C 123 ALA PRO GLY GLU ASP ARG ALA PHE VAL THR SER ILE SER SEQRES 5 C 123 ARG ALA ALA TYR THR TYR TYR ALA ASP SER VAL LYS GLY SEQRES 6 C 123 ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN MET VAL SEQRES 7 C 123 SER LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR ALA SEQRES 8 C 123 VAL TYR VAL CYS ALA GLY LYS GLY GLN GLY GLY THR TRP SEQRES 9 C 123 ASP TYR TRP GLY GLN GLY THR GLN VAL THR VAL SER SER SEQRES 10 C 123 HIS HIS HIS HIS HIS HIS SEQRES 1 D 123 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 D 123 ALA GLY GLY SER LEU ARG LEU SER CYS ALA ALA SER GLY SEQRES 3 D 123 ARG THR PHE SER LEU THR THR MET GLY TRP PHE ARG GLN SEQRES 4 D 123 ALA PRO GLY GLU ASP ARG ALA PHE VAL THR SER ILE SER SEQRES 5 D 123 ARG ALA ALA TYR THR TYR TYR ALA ASP SER VAL LYS GLY SEQRES 6 D 123 ARG PHE THR ILE SER ARG ASP ASN ALA LYS ASN MET VAL SEQRES 7 D 123 SER LEU GLN MET ASN SER LEU LYS PRO GLU ASP THR ALA SEQRES 8 D 123 VAL TYR VAL CYS ALA GLY LYS GLY GLN GLY GLY THR TRP SEQRES 9 D 123 ASP TYR TRP GLY GLN GLY THR GLN VAL THR VAL SER SER SEQRES 10 D 123 HIS HIS HIS HIS HIS HIS HET EDO A 601 4 HET EDO A 602 4 HET TRS A 603 8 HET EDO A 604 4 HET EDO B 601 4 HET EDO B 602 4 HET EDO B 603 4 HET EDO B 604 4 HET EDO C 700 4 HET EDO C 701 4 HETNAM EDO 1,2-ETHANEDIOL HETNAM TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL HETSYN EDO ETHYLENE GLYCOL HETSYN TRS TRIS BUFFER FORMUL 5 EDO 9(C2 H6 O2) FORMUL 7 TRS C4 H12 N O3 1+ FORMUL 15 HOH *712(H2 O) HELIX 1 AA1 GLN A 236 CYS A 240 5 5 HELIX 2 AA2 SER A 282 VAL A 286 5 5 HELIX 3 AA3 ALA A 368 GLN A 371 5 4 HELIX 4 AA4 PRO A 454 ASN A 464 1 11 HELIX 5 AA5 GLN B 236 CYS B 240 5 5 HELIX 6 AA6 SER B 282 VAL B 286 5 5 HELIX 7 AA7 ALA B 368 GLN B 371 5 4 HELIX 8 AA8 PRO B 454 SER B 463 1 10 HELIX 9 AA9 THR C 28 LEU C 31 5 4 HELIX 10 AB1 ASP C 61 LYS C 64 5 4 HELIX 11 AB2 LYS C 86 THR C 90 5 5 HELIX 12 AB3 THR D 28 LEU D 31 5 4 HELIX 13 AB4 ASP D 61 LYS D 64 5 4 HELIX 14 AB5 LYS D 86 THR D 90 5 5 SHEET 1 AA1 4 ALA A 444 CYS A 451 0 SHEET 2 AA1 4 ARG A 431 ILE A 439 -1 N MET A 436 O GLU A 447 SHEET 3 AA1 4 GLY A 251 VAL A 254 -1 N LEU A 253 O ARG A 431 SHEET 4 AA1 4 LEU A 507 THR A 508 -1 O LEU A 507 N VAL A 254 SHEET 1 AA2 7 PHE A 289 GLN A 298 0 SHEET 2 AA2 7 GLY A 302 ILE A 310 -1 O THR A 308 N GLU A 292 SHEET 3 AA2 7 ARG A 373 THR A 379 -1 O VAL A 374 N PHE A 307 SHEET 4 AA2 7 VAL A 352 ILE A 358 -1 N GLU A 356 O SER A 377 SHEET 5 AA2 7 SER A 332 THR A 341 -1 N LEU A 335 O MET A 357 SHEET 6 AA2 7 GLY A 389 GLN A 402 -1 O TYR A 399 N GLN A 334 SHEET 7 AA2 7 PHE A 289 GLN A 298 -1 N ALA A 293 O GLY A 389 SHEET 1 AA3 5 LYS A 349 LEU A 350 0 SHEET 2 AA3 5 ALA B 444 CYS B 451 -1 O ALA B 444 N LEU A 350 SHEET 3 AA3 5 ARG B 431 GLN B 438 -1 N MET B 436 O GLU B 447 SHEET 4 AA3 5 GLY B 251 VAL B 254 -1 N LEU B 253 O ARG B 431 SHEET 5 AA3 5 LEU B 507 PHE B 509 -1 O PHE B 509 N LEU B 252 SHEET 1 AA4 5 GLU A 427 LEU A 429 0 SHEET 2 AA4 5 ILE A 497 SER A 500 -1 O LEU A 499 N VAL A 428 SHEET 3 AA4 5 LEU A 485 TYR A 492 -1 N LYS A 490 O ALA A 498 SHEET 4 AA4 5 ALA A 472 ASN A 479 -1 N TYR A 477 O LEU A 486 SHEET 5 AA4 5 GLY A 513 VAL A 521 -1 O SER A 519 N LEU A 474 SHEET 1 AA5 7 PHE B 289 GLN B 298 0 SHEET 2 AA5 7 GLY B 302 ILE B 310 -1 O GLY B 302 N GLN B 298 SHEET 3 AA5 7 ARG B 373 ALA B 381 -1 O ALA B 376 N ALA B 305 SHEET 4 AA5 7 VAL B 352 LEU B 359 -1 N THR B 354 O ALA B 380 SHEET 5 AA5 7 SER B 332 THR B 341 -1 N VAL B 339 O THR B 353 SHEET 6 AA5 7 GLY B 389 GLN B 402 -1 O TYR B 399 N GLN B 334 SHEET 7 AA5 7 PHE B 289 GLN B 298 -1 N PHE B 289 O ALA B 393 SHEET 1 AA6 5 GLU B 427 LEU B 429 0 SHEET 2 AA6 5 ILE B 497 SER B 500 -1 O LEU B 499 N VAL B 428 SHEET 3 AA6 5 LEU B 485 TYR B 492 -1 N LYS B 490 O ALA B 498 SHEET 4 AA6 5 ALA B 472 ASN B 479 -1 N TYR B 477 O LEU B 486 SHEET 5 AA6 5 GLY B 513 VAL B 521 -1 O SER B 519 N LEU B 474 SHEET 1 AA7 4 VAL C 2 SER C 7 0 SHEET 2 AA7 4 LEU C 18 GLY C 26 -1 O ALA C 23 N GLN C 5 SHEET 3 AA7 4 MET C 77 MET C 82 -1 O MET C 82 N LEU C 18 SHEET 4 AA7 4 PHE C 67 ASP C 72 -1 N THR C 68 O GLN C 81 SHEET 1 AA8 6 GLY C 10 GLN C 13 0 SHEET 2 AA8 6 THR C 111 SER C 116 1 O THR C 114 N GLY C 10 SHEET 3 AA8 6 ALA C 91 LYS C 98 -1 N TYR C 93 O THR C 111 SHEET 4 AA8 6 MET C 34 GLN C 39 -1 N PHE C 37 O VAL C 94 SHEET 5 AA8 6 ALA C 46 ILE C 51 -1 O ILE C 51 N MET C 34 SHEET 6 AA8 6 THR C 57 TYR C 59 -1 O TYR C 58 N SER C 50 SHEET 1 AA9 4 GLY C 10 GLN C 13 0 SHEET 2 AA9 4 THR C 111 SER C 116 1 O THR C 114 N GLY C 10 SHEET 3 AA9 4 ALA C 91 LYS C 98 -1 N TYR C 93 O THR C 111 SHEET 4 AA9 4 TRP C 104 TRP C 107 -1 O TYR C 106 N GLY C 97 SHEET 1 AB1 4 VAL D 2 GLY D 8 0 SHEET 2 AB1 4 LEU D 18 GLY D 26 -1 O SER D 25 N GLN D 3 SHEET 3 AB1 4 MET D 77 MET D 82 -1 O LEU D 80 N LEU D 20 SHEET 4 AB1 4 PHE D 67 ASP D 72 -1 N THR D 68 O GLN D 81 SHEET 1 AB2 6 GLY D 10 GLN D 13 0 SHEET 2 AB2 6 THR D 111 SER D 116 1 O THR D 114 N GLY D 10 SHEET 3 AB2 6 ALA D 91 LYS D 98 -1 N TYR D 93 O THR D 111 SHEET 4 AB2 6 MET D 34 GLN D 39 -1 N PHE D 37 O VAL D 94 SHEET 5 AB2 6 ALA D 46 ILE D 51 -1 O ILE D 51 N MET D 34 SHEET 6 AB2 6 THR D 57 TYR D 59 -1 O TYR D 58 N SER D 50 SHEET 1 AB3 4 GLY D 10 GLN D 13 0 SHEET 2 AB3 4 THR D 111 SER D 116 1 O THR D 114 N GLY D 10 SHEET 3 AB3 4 ALA D 91 LYS D 98 -1 N TYR D 93 O THR D 111 SHEET 4 AB3 4 TRP D 104 TRP D 107 -1 O TYR D 106 N GLY D 97 SSBOND 1 CYS C 22 CYS C 95 1555 1555 2.14 SSBOND 2 CYS D 22 CYS D 95 1555 1555 2.13 CISPEP 1 GLY A 360 PRO A 361 0 -7.72 CISPEP 2 GLY A 421 PRO A 422 0 6.47 CISPEP 3 GLY B 421 PRO B 422 0 4.62 SITE 1 AC1 7 TYR A 295 VAL A 339 LYS A 351 THR A 353 SITE 2 AC1 7 VAL A 391 HOH A 726 HOH A 839 SITE 1 AC2 5 LEU A 258 ASP A 403 ALA A 448 ILE A 449 SITE 2 AC2 5 ASP A 450 SITE 1 AC3 9 TYR A 295 LYS A 296 PHE A 297 GLU A 303 SITE 2 AC3 9 SER A 383 ASP A 385 LEU A 386 ASP D 72 SITE 3 AC3 9 LYS D 75 SITE 1 AC4 6 GLU A 456 SER A 459 TRP A 460 HOH A 722 SITE 2 AC4 6 SER B 459 SER B 463 SITE 1 AC5 7 GLN A 340 THR A 343 ALA B 247 TYR B 250 SITE 2 AC5 7 TYR B 435 HOH B 754 HOH B 876 SITE 1 AC6 6 LEU B 258 ASP B 403 ARG B 433 ALA B 448 SITE 2 AC6 6 ILE B 449 ASP B 450 SITE 1 AC7 6 LEU A 239 PRO B 280 ILE B 281 SER B 282 SITE 2 AC7 6 TRP B 285 GLY D 101 SITE 1 AC8 2 THR B 346 HOH B 703 SITE 1 AC9 7 SER C 70 ARG C 71 ASP C 72 MET C 77 SITE 2 AC9 7 SER C 79 HOH C 822 HOH C 856 SITE 1 AD1 5 TYR C 56 THR C 57 HOH C 818 HOH C 840 SITE 2 AD1 5 HOH C 850 CRYST1 101.720 101.720 228.520 90.00 90.00 90.00 P 41 21 2 16 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 0.009831 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009831 0.000000 0.00000 SCALE3 0.000000 0.000000 0.004376 0.00000