HEADER VIRAL PROTEIN 23-JAN-20 6XW4 TITLE CRYSTAL STRUCTURE OF MURINE NOROVIRUS P DOMAIN IN COMPLEX WITH TITLE 2 NANOBODY NB-5867 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-5867; 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_COMMON: ALPACA; SOURCE 10 ORGANISM_TAXID: 30538; SOURCE 11 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 12 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 13 EXPRESSION_SYSTEM_VARIANT: WK6; SOURCE 14 EXPRESSION_SYSTEM_VECTOR_TYPE: 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 6XW4 1 REMARK REVDAT 3 01-JUL-20 6XW4 1 JRNL REVDAT 2 06-MAY-20 6XW4 1 JRNL REVDAT 1 22-APR-20 6XW4 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. 2.19 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.19 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.38 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 59137 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) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.218 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3118 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) : 2.19 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.25 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3992 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.07 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 201 REMARK 3 BIN FREE R VALUE : 0.2850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6518 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 36 REMARK 3 SOLVENT ATOMS : 445 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.42 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.38 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.43000 REMARK 3 B22 (A**2) : -1.36000 REMARK 3 B33 (A**2) : -2.07000 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): 0.184 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.168 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.123 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.071 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6721 ; 0.010 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 6093 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9162 ; 1.618 ; 1.651 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14103 ; 1.282 ; 1.565 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 845 ; 8.283 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 338 ;32.331 ;21.834 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 997 ;13.860 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 44 ;16.127 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 875 ; 0.066 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7617 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1475 ; 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 : 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6XW4 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_1292106286. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-MAY-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 : ID30B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97856 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 X 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 62254 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.190 REMARK 200 RESOLUTION RANGE LOW (A) : 47.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 6.503 REMARK 200 R MERGE (I) : 0.13800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.1100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.19 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.25 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.5 REMARK 200 DATA REDUNDANCY IN SHELL : 6.24 REMARK 200 R MERGE FOR SHELL (I) : 0.75300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.560 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 (%): 61.19 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.0 M LITHIUM CHLORIDE 0.1 M CITRIC REMARK 280 ACID PH 5.0 20%(W/V) PEG 6000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K 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 37.66500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 73.33000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 54.52000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 73.33000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 37.66500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 54.52000 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 9720 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 31580 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 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 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 ARG A 228 REMARK 465 GLY A 531 REMARK 465 SER A 532 REMARK 465 LEU A 533 REMARK 465 ARG B 228 REMARK 465 GLY B 531 REMARK 465 SER B 532 REMARK 465 LEU B 533 REMARK 465 SER C 122 REMARK 465 HIS C 123 REMARK 465 HIS C 124 REMARK 465 HIS C 125 REMARK 465 HIS C 126 REMARK 465 HIS C 127 REMARK 465 HIS C 128 REMARK 465 HIS D 123 REMARK 465 HIS D 124 REMARK 465 HIS D 125 REMARK 465 HIS D 126 REMARK 465 HIS D 127 REMARK 465 HIS D 128 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 OE2 GLU A 338 OE2 GLU B 338 2.15 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 321 52.04 -94.93 REMARK 500 LYS A 349 -60.80 -92.58 REMARK 500 ASN A 364 -103.34 -124.63 REMARK 500 ASN A 409 45.11 -156.16 REMARK 500 GLN B 263 43.59 -103.10 REMARK 500 SER B 299 125.40 -37.55 REMARK 500 THR B 363 14.49 83.06 REMARK 500 ASN B 364 -90.11 -112.96 REMARK 500 ASN B 409 51.90 -152.53 REMARK 500 ARG C 30 -179.33 -172.11 REMARK 500 LYS C 74 115.81 -39.76 REMARK 500 ILE C 103 -164.14 -125.59 REMARK 500 ARG D 30 -178.45 -173.49 REMARK 500 ARG D 67 -52.88 -121.82 REMARK 500 LYS D 74 122.48 -39.32 REMARK 500 ALA D 92 168.41 174.39 REMARK 500 ALA D 104 72.10 -119.82 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 EDO 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 A 605 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 702 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 703 DBREF 6XW4 A 228 533 UNP Q80J94 Q80J94_9CALI 228 533 DBREF 6XW4 B 228 533 UNP Q80J94 Q80J94_9CALI 228 533 DBREF 6XW4 C 1 128 PDB 6XW4 6XW4 1 128 DBREF 6XW4 D 1 128 PDB 6XW4 6XW4 1 128 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 128 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 C 128 ALA GLY GLY SER LEU ARG LEU SER CYS ALA LYS SER GLY SEQRES 3 C 128 ARG THR PHE ARG ALA TYR ALA MET GLY TRP PHE ARG GLN SEQRES 4 C 128 ALA PRO GLY LYS GLU ARG GLU PHE VAL ALA ALA ILE ASP SEQRES 5 C 128 TRP SER ALA ALA ILE THR ASN TYR ALA ASP SER VAL LYS SEQRES 6 C 128 GLY ARG PHE THR ILE LEU ARG ASP LYS GLY MET ASN THR SEQRES 7 C 128 ALA TYR LEU GLN MET ASN SER LEU GLU PRO GLU ASP THR SEQRES 8 C 128 ALA VAL TYR TYR CYS ALA ALA THR TYR SER THR ILE ALA SEQRES 9 C 128 PRO ARG THR SER TYR ASP PHE TRP GLY GLN GLY THR GLN SEQRES 10 C 128 VAL THR VAL SER SER HIS HIS HIS HIS HIS HIS SEQRES 1 D 128 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 D 128 ALA GLY GLY SER LEU ARG LEU SER CYS ALA LYS SER GLY SEQRES 3 D 128 ARG THR PHE ARG ALA TYR ALA MET GLY TRP PHE ARG GLN SEQRES 4 D 128 ALA PRO GLY LYS GLU ARG GLU PHE VAL ALA ALA ILE ASP SEQRES 5 D 128 TRP SER ALA ALA ILE THR ASN TYR ALA ASP SER VAL LYS SEQRES 6 D 128 GLY ARG PHE THR ILE LEU ARG ASP LYS GLY MET ASN THR SEQRES 7 D 128 ALA TYR LEU GLN MET ASN SER LEU GLU PRO GLU ASP THR SEQRES 8 D 128 ALA VAL TYR TYR CYS ALA ALA THR TYR SER THR ILE ALA SEQRES 9 D 128 PRO ARG THR SER TYR ASP PHE TRP GLY GLN GLY THR GLN SEQRES 10 D 128 VAL THR VAL SER SER HIS HIS HIS HIS HIS HIS HET EDO A 601 4 HET EDO A 602 4 HET EDO A 603 4 HET EDO A 604 4 HET EDO A 605 4 HET EDO A 606 4 HET EDO B 701 4 HET EDO B 702 4 HET EDO B 703 4 HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 EDO 9(C2 H6 O2) FORMUL 14 HOH *445(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 PRO B 454 ASN B 464 1 11 HELIX 8 AA8 ASP C 62 LYS C 65 5 4 HELIX 9 AA9 GLU C 87 THR C 91 5 5 HELIX 10 AB1 ASP D 62 LYS D 65 5 4 HELIX 11 AB2 GLU D 87 THR D 91 5 5 SHEET 1 AA1 4 GLU A 447 CYS A 451 0 SHEET 2 AA1 4 ARG A 431 MET A 436 -1 N THR A 434 O ILE A 449 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 8 GLN A 438 ILE A 439 0 SHEET 2 AA2 8 GLY A 389 GLN A 402 1 N ILE A 398 O ILE A 439 SHEET 3 AA2 8 SER A 332 GLU A 342 -1 N GLN A 334 O TYR A 399 SHEET 4 AA2 8 LEU A 350 GLY A 360 -1 O LYS A 351 N THR A 341 SHEET 5 AA2 8 ARG A 373 VAL A 378 -1 O SER A 377 N GLU A 356 SHEET 6 AA2 8 GLY A 302 ILE A 310 -1 N PHE A 307 O VAL A 374 SHEET 7 AA2 8 PHE A 289 GLN A 298 -1 N LYS A 296 O VAL A 304 SHEET 8 AA2 8 GLY A 389 GLN A 402 -1 O ALA A 393 N PHE A 289 SHEET 1 AA3 5 GLU A 427 LEU A 429 0 SHEET 2 AA3 5 ILE A 497 SER A 500 -1 O LEU A 499 N VAL A 428 SHEET 3 AA3 5 LEU A 485 TYR A 492 -1 N LYS A 490 O ALA A 498 SHEET 4 AA3 5 ALA A 472 ASN A 479 -1 N LEU A 475 O CYS A 489 SHEET 5 AA3 5 GLY A 513 VAL A 521 -1 O VAL A 518 N LEU A 474 SHEET 1 AA4 4 GLU B 447 CYS B 451 0 SHEET 2 AA4 4 ARG B 431 MET B 436 -1 N PHE B 432 O CYS B 451 SHEET 3 AA4 4 GLY B 251 VAL B 254 -1 N LEU B 253 O ARG B 431 SHEET 4 AA4 4 LEU B 507 PHE B 509 -1 O PHE B 509 N LEU B 252 SHEET 1 AA5 8 GLN B 438 ILE B 439 0 SHEET 2 AA5 8 GLY B 389 GLN B 402 1 N ILE B 398 O ILE B 439 SHEET 3 AA5 8 SER B 332 GLU B 342 -1 N GLN B 334 O TYR B 399 SHEET 4 AA5 8 LEU B 350 GLY B 360 -1 O LYS B 351 N THR B 341 SHEET 5 AA5 8 ARG B 373 VAL B 378 -1 O SER B 377 N GLU B 356 SHEET 6 AA5 8 GLY B 302 ILE B 310 -1 N PHE B 307 O VAL B 374 SHEET 7 AA5 8 PHE B 289 GLN B 298 -1 N LYS B 296 O VAL B 304 SHEET 8 AA5 8 GLY B 389 GLN B 402 -1 O GLY B 389 N ALA B 293 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 LEU B 475 O CYS B 489 SHEET 5 AA6 5 GLY B 513 VAL B 521 -1 O SER B 519 N LEU B 474 SHEET 1 AA7 4 GLN C 3 SER C 7 0 SHEET 2 AA7 4 LEU C 18 SER C 25 -1 O SER C 25 N GLN C 3 SHEET 3 AA7 4 THR C 78 MET C 83 -1 O MET C 83 N LEU C 18 SHEET 4 AA7 4 PHE C 68 ARG C 72 -1 N THR C 69 O GLN C 82 SHEET 1 AA8 6 GLY C 10 VAL C 12 0 SHEET 2 AA8 6 THR C 116 VAL C 120 1 O GLN C 117 N GLY C 10 SHEET 3 AA8 6 ALA C 92 TYR C 100 -1 N ALA C 92 O VAL C 118 SHEET 4 AA8 6 TYR C 32 GLN C 39 -1 N PHE C 37 O TYR C 95 SHEET 5 AA8 6 GLU C 46 ILE C 51 -1 O GLU C 46 N ARG C 38 SHEET 6 AA8 6 THR C 58 TYR C 60 -1 O ASN C 59 N ALA C 50 SHEET 1 AA9 4 GLY C 10 VAL C 12 0 SHEET 2 AA9 4 THR C 116 VAL C 120 1 O GLN C 117 N GLY C 10 SHEET 3 AA9 4 ALA C 92 TYR C 100 -1 N ALA C 92 O VAL C 118 SHEET 4 AA9 4 PHE C 111 TRP C 112 -1 O PHE C 111 N ALA C 98 SHEET 1 AB1 4 GLN D 3 SER D 7 0 SHEET 2 AB1 4 LEU D 18 SER D 25 -1 O SER D 25 N GLN D 3 SHEET 3 AB1 4 THR D 78 MET D 83 -1 O MET D 83 N LEU D 18 SHEET 4 AB1 4 PHE D 68 ARG D 72 -1 N THR D 69 O GLN D 82 SHEET 1 AB2 6 LEU D 11 GLN D 13 0 SHEET 2 AB2 6 THR D 116 SER D 121 1 O SER D 121 N VAL D 12 SHEET 3 AB2 6 ALA D 92 TYR D 100 -1 N TYR D 94 O THR D 116 SHEET 4 AB2 6 TYR D 32 GLN D 39 -1 N GLY D 35 O ALA D 97 SHEET 5 AB2 6 GLU D 46 ILE D 51 -1 O GLU D 46 N ARG D 38 SHEET 6 AB2 6 THR D 58 TYR D 60 -1 O ASN D 59 N ALA D 50 SHEET 1 AB3 4 LEU D 11 GLN D 13 0 SHEET 2 AB3 4 THR D 116 SER D 121 1 O SER D 121 N VAL D 12 SHEET 3 AB3 4 ALA D 92 TYR D 100 -1 N TYR D 94 O THR D 116 SHEET 4 AB3 4 PHE D 111 TRP D 112 -1 O PHE D 111 N ALA D 98 SSBOND 1 CYS C 22 CYS C 96 1555 1555 2.04 SSBOND 2 CYS D 22 CYS D 96 1555 1555 2.09 CISPEP 1 GLY A 360 PRO A 361 0 3.04 CISPEP 2 GLY A 421 PRO A 422 0 2.58 CISPEP 3 GLY B 360 PRO B 361 0 6.80 CISPEP 4 GLY B 421 PRO B 422 0 4.88 SITE 1 AC1 5 PRO A 361 THR A 362 ILE A 405 PRO A 406 SITE 2 AC1 5 GLU A 407 SITE 1 AC2 6 LEU A 258 ASP A 403 ARG A 433 ALA A 448 SITE 2 AC2 6 ILE A 449 ASP A 450 SITE 1 AC3 6 TYR A 295 GLN A 340 THR A 341 VAL A 387 SITE 2 AC3 6 ARG A 390 VAL A 391 SITE 1 AC4 3 TYR A 525 GLN A 526 GLN B 469 SITE 1 AC5 6 SER A 284 ARG A 392 EDO A 606 HOH A 746 SITE 2 AC5 6 PRO B 246 EDO B 701 SITE 1 AC6 7 GLU A 338 VAL A 394 PRO A 395 EDO A 605 SITE 2 AC6 7 GLU B 338 PRO B 395 EDO B 701 SITE 1 AC7 6 PRO A 246 EDO A 605 EDO A 606 SER B 284 SITE 2 AC7 6 ARG B 392 HOH B 844 SITE 1 AC8 8 TYR B 295 GLN B 340 THR B 341 VAL B 387 SITE 2 AC8 8 ARG B 390 VAL B 391 HOH B 802 HOH B 810 SITE 1 AC9 5 LEU B 258 ASP B 403 ALA B 448 ILE B 449 SITE 2 AC9 5 ASP B 450 CRYST1 75.330 109.040 146.660 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 0.013275 0.000000 0.000000 0.00000 SCALE2 0.000000 0.009171 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006818 0.00000