HEADER VIRAL PROTEIN 23-JAN-20 6XW6 TITLE CRYSTAL STRUCTURE OF MURINE NOROVIRUS P DOMAIN IN COMPLEX WITH TITLE 2 NANOBODY NB-5853 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-5853; COMPND 7 CHAIN: D, C; 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 6XW6 1 LINK REVDAT 3 01-JUL-20 6XW6 1 JRNL REVDAT 2 06-MAY-20 6XW6 1 JRNL REVDAT 1 22-APR-20 6XW6 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. 1.96 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) : 1.96 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.58 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 58492 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) : 0.202 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.300 REMARK 3 FREE R VALUE TEST SET COUNT : 3280 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) : 1.96 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.01 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4252 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2490 REMARK 3 BIN FREE R VALUE SET COUNT : 211 REMARK 3 BIN FREE R VALUE : 0.3180 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6605 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 15 REMARK 3 SOLVENT ATOMS : 455 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 28.75 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 26.74 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.20000 REMARK 3 B22 (A**2) : -1.73000 REMARK 3 B33 (A**2) : 0.74000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.06000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.194 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.173 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.135 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.850 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.940 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.903 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6794 ; 0.008 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 6144 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9273 ; 1.548 ; 1.649 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14216 ; 1.279 ; 1.567 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 862 ; 8.220 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 351 ;31.837 ;21.510 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1012 ;13.560 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 50 ;19.188 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 885 ; 0.064 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7741 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1501 ; 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 6XW6 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_1292106271. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-NOV-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 : MASSIF-3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.967700 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER X 4M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 61772 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.960 REMARK 200 RESOLUTION RANGE LOW (A) : 38.580 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 6.463 REMARK 200 R MERGE (I) : 0.14300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.9700 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.96 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.01 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.0 REMARK 200 DATA REDUNDANCY IN SHELL : 6.44 REMARK 200 R MERGE FOR SHELL (I) : 0.74300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.250 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 (%): 46.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M LITHIUM SULFATE 0.1 M SODIUM REMARK 280 ACETATE PH 4.5 30%(W/V) PEG 8000, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 42.64500 REMARK 290 SMTRY3 2 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: 8250 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32250 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -34.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, D, C 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 GLY A 531 REMARK 465 SER A 532 REMARK 465 LEU A 533 REMARK 465 GLY B 531 REMARK 465 SER B 532 REMARK 465 LEU B 533 REMARK 465 GLN D 1 REMARK 465 SER D 128 REMARK 465 HIS D 129 REMARK 465 HIS D 130 REMARK 465 HIS D 131 REMARK 465 HIS D 132 REMARK 465 HIS D 133 REMARK 465 HIS D 134 REMARK 465 GLN C 1 REMARK 465 SER C 128 REMARK 465 HIS C 129 REMARK 465 HIS C 130 REMARK 465 HIS C 131 REMARK 465 HIS C 132 REMARK 465 HIS C 133 REMARK 465 HIS C 134 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 526 CG CD OE1 NE2 REMARK 470 LYS B 345 CG CD CE NZ REMARK 470 SER D 127 OG REMARK 470 ASP C 62 CG OD1 OD2 REMARK 470 SER C 127 OG 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 NH1 ARG A 396 OE2 GLU B 338 1.98 REMARK 500 OE2 GLU A 338 OE2 GLU B 338 2.00 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 41.62 -102.58 REMARK 500 ASP A 321 37.28 -94.08 REMARK 500 LYS A 349 -61.57 -158.61 REMARK 500 ASN A 409 45.70 -149.10 REMARK 500 ARG A 437 129.78 -37.95 REMARK 500 ALA A 442 -40.10 -132.83 REMARK 500 ALA A 465 69.40 32.72 REMARK 500 GLN A 469 -81.11 -94.81 REMARK 500 VAL A 518 -61.78 -91.81 REMARK 500 GLN B 263 46.96 -106.52 REMARK 500 THR B 301 -45.40 -135.03 REMARK 500 LYS B 349 -74.94 -157.64 REMARK 500 SER B 383 136.04 -37.66 REMARK 500 ASN B 409 48.87 -161.39 REMARK 500 ALA B 465 75.84 36.44 REMARK 500 ALA D 14 134.13 -39.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 602 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 366 OD2 REMARK 620 2 ASP A 410 OD1 83.6 REMARK 620 3 HOH A 709 O 68.5 87.6 REMARK 620 4 HOH A 807 O 94.7 86.7 162.8 REMARK 620 5 HOH A 852 O 85.0 168.7 88.4 94.1 REMARK 620 6 HOH A 860 O 170.0 89.4 104.2 91.9 101.9 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 601 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 438 OE1 REMARK 620 2 ASP A 440 OD2 92.0 REMARK 620 3 HOH A 708 O 95.5 89.6 REMARK 620 4 HOH A 728 O 84.7 84.1 173.7 REMARK 620 5 HOH A 802 O 91.4 175.7 92.7 93.7 REMARK 620 6 HOH A 826 O 170.7 89.1 93.8 86.2 87.1 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 601 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN B 438 OE1 REMARK 620 2 ASP B 440 OD2 95.7 REMARK 620 3 HOH B 722 O 98.0 95.8 REMARK 620 4 HOH B 777 O 92.3 87.4 168.8 REMARK 620 5 HOH B 816 O 90.7 172.4 87.4 88.1 REMARK 620 6 HOH B 835 O 171.5 87.3 89.5 79.9 85.8 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG 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 MG B 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 602 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO B 603 DBREF 6XW6 A 228 533 UNP Q80J94 Q80J94_9CALI 228 533 DBREF 6XW6 B 228 533 UNP Q80J94 Q80J94_9CALI 228 533 DBREF 6XW6 D 1 134 PDB 6XW6 6XW6 1 134 DBREF 6XW6 C 1 134 PDB 6XW6 6XW6 1 134 SEQADV 6XW6 SER A 227 UNP Q80J94 EXPRESSION TAG SEQADV 6XW6 SER B 227 UNP Q80J94 EXPRESSION TAG SEQRES 1 A 307 SER ARG MET VAL ASP LEU PRO VAL ILE GLN PRO ARG LEU SEQRES 2 A 307 CYS THR HIS ALA ARG TRP PRO ALA PRO VAL TYR GLY LEU SEQRES 3 A 307 LEU VAL ASP PRO SER LEU PRO SER ASN PRO GLN TRP GLN SEQRES 4 A 307 ASN GLY ARG VAL HIS VAL ASP GLY THR LEU LEU GLY THR SEQRES 5 A 307 THR PRO ILE SER GLY SER TRP VAL SER CYS PHE ALA ALA SEQRES 6 A 307 GLU ALA ALA TYR LYS PHE GLN SER GLY THR GLY GLU VAL SEQRES 7 A 307 ALA THR PHE THR LEU ILE GLU GLN ASP GLY SER ALA TYR SEQRES 8 A 307 VAL PRO GLY ASP ARG ALA ALA PRO LEU GLY TYR PRO ASP SEQRES 9 A 307 PHE SER GLY GLN LEU GLU ILE GLU VAL GLN THR GLU THR SEQRES 10 A 307 THR LYS THR GLY ASP LYS LEU LYS VAL THR THR PHE GLU SEQRES 11 A 307 MET ILE LEU GLY PRO THR THR ASN ALA ASP GLN ALA PRO SEQRES 12 A 307 TYR GLN GLY ARG VAL PHE ALA SER VAL THR ALA ALA ALA SEQRES 13 A 307 SER LEU ASP LEU VAL ASP GLY ARG VAL ARG ALA VAL PRO SEQRES 14 A 307 ARG SER ILE TYR GLY PHE GLN ASP THR ILE PRO GLU TYR SEQRES 15 A 307 ASN ASP GLY LEU LEU VAL PRO LEU ALA PRO PRO ILE GLY SEQRES 16 A 307 PRO PHE LEU PRO GLY GLU VAL LEU LEU ARG PHE ARG THR SEQRES 17 A 307 TYR MET ARG GLN ILE ASP THR ALA ASP ALA ALA ALA GLU SEQRES 18 A 307 ALA ILE ASP CYS ALA LEU PRO GLN GLU PHE VAL SER TRP SEQRES 19 A 307 PHE ALA SER ASN ALA PHE THR VAL GLN SER GLU ALA LEU SEQRES 20 A 307 LEU LEU ARG TYR ARG ASN THR LEU THR GLY GLN LEU LEU SEQRES 21 A 307 PHE GLU CYS LYS LEU TYR ASN GLU GLY TYR ILE ALA LEU SEQRES 22 A 307 SER TYR SER GLY SER GLY PRO LEU THR PHE PRO THR ASP SEQRES 23 A 307 GLY ILE PHE GLU VAL VAL SER TRP VAL PRO ARG LEU TYR SEQRES 24 A 307 GLN LEU ALA SER VAL GLY SER LEU SEQRES 1 B 307 SER ARG MET VAL ASP LEU PRO VAL ILE GLN PRO ARG LEU SEQRES 2 B 307 CYS THR HIS ALA ARG TRP PRO ALA PRO VAL TYR GLY LEU SEQRES 3 B 307 LEU VAL ASP PRO SER LEU PRO SER ASN PRO GLN TRP GLN SEQRES 4 B 307 ASN GLY ARG VAL HIS VAL ASP GLY THR LEU LEU GLY THR SEQRES 5 B 307 THR PRO ILE SER GLY SER TRP VAL SER CYS PHE ALA ALA SEQRES 6 B 307 GLU ALA ALA TYR LYS PHE GLN SER GLY THR GLY GLU VAL SEQRES 7 B 307 ALA THR PHE THR LEU ILE GLU GLN ASP GLY SER ALA TYR SEQRES 8 B 307 VAL PRO GLY ASP ARG ALA ALA PRO LEU GLY TYR PRO ASP SEQRES 9 B 307 PHE SER GLY GLN LEU GLU ILE GLU VAL GLN THR GLU THR SEQRES 10 B 307 THR LYS THR GLY ASP LYS LEU LYS VAL THR THR PHE GLU SEQRES 11 B 307 MET ILE LEU GLY PRO THR THR ASN ALA ASP GLN ALA PRO SEQRES 12 B 307 TYR GLN GLY ARG VAL PHE ALA SER VAL THR ALA ALA ALA SEQRES 13 B 307 SER LEU ASP LEU VAL ASP GLY ARG VAL ARG ALA VAL PRO SEQRES 14 B 307 ARG SER ILE TYR GLY PHE GLN ASP THR ILE PRO GLU TYR SEQRES 15 B 307 ASN ASP GLY LEU LEU VAL PRO LEU ALA PRO PRO ILE GLY SEQRES 16 B 307 PRO PHE LEU PRO GLY GLU VAL LEU LEU ARG PHE ARG THR SEQRES 17 B 307 TYR MET ARG GLN ILE ASP THR ALA ASP ALA ALA ALA GLU SEQRES 18 B 307 ALA ILE ASP CYS ALA LEU PRO GLN GLU PHE VAL SER TRP SEQRES 19 B 307 PHE ALA SER ASN ALA PHE THR VAL GLN SER GLU ALA LEU SEQRES 20 B 307 LEU LEU ARG TYR ARG ASN THR LEU THR GLY GLN LEU LEU SEQRES 21 B 307 PHE GLU CYS LYS LEU TYR ASN GLU GLY TYR ILE ALA LEU SEQRES 22 B 307 SER TYR SER GLY SER GLY PRO LEU THR PHE PRO THR ASP SEQRES 23 B 307 GLY ILE PHE GLU VAL VAL SER TRP VAL PRO ARG LEU TYR SEQRES 24 B 307 GLN LEU ALA SER VAL GLY SER LEU SEQRES 1 D 134 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 D 134 ALA GLY ASP SER LEU ARG VAL SER CYS ALA ALA SER GLY SEQRES 3 D 134 ARG THR ILE SER SER SER PRO MET GLY TRP PHE ARG GLN SEQRES 4 D 134 ALA PRO GLY LYS GLU ARG GLU PHE VAL ALA ALA ILE SER SEQRES 5 D 134 GLY ASN GLY GLY ASN THR TYR TYR LEU ASP SER VAL LYS SEQRES 6 D 134 GLY ARG PHE THR THR SER ARG ASP ASN ALA LYS ASN THR SEQRES 7 D 134 VAL TYR LEU GLN LEU ASN ASN LEU LYS PRO GLU ASP THR SEQRES 8 D 134 ALA ILE TYR TYR CYS ALA ALA ARG SER ARG PHE SER ALA SEQRES 9 D 134 MET HIS LEU ALA TYR ARG ARG LEU VAL ASP TYR ASP ASP SEQRES 10 D 134 TRP GLY GLN GLY THR GLN VAL THR VAL SER SER HIS HIS SEQRES 11 D 134 HIS HIS HIS HIS SEQRES 1 C 134 GLN VAL GLN LEU GLN GLU SER GLY GLY GLY LEU VAL GLN SEQRES 2 C 134 ALA GLY ASP SER LEU ARG VAL SER CYS ALA ALA SER GLY SEQRES 3 C 134 ARG THR ILE SER SER SER PRO MET GLY TRP PHE ARG GLN SEQRES 4 C 134 ALA PRO GLY LYS GLU ARG GLU PHE VAL ALA ALA ILE SER SEQRES 5 C 134 GLY ASN GLY GLY ASN THR TYR TYR LEU ASP SER VAL LYS SEQRES 6 C 134 GLY ARG PHE THR THR SER ARG ASP ASN ALA LYS ASN THR SEQRES 7 C 134 VAL TYR LEU GLN LEU ASN ASN LEU LYS PRO GLU ASP THR SEQRES 8 C 134 ALA ILE TYR TYR CYS ALA ALA ARG SER ARG PHE SER ALA SEQRES 9 C 134 MET HIS LEU ALA TYR ARG ARG LEU VAL ASP TYR ASP ASP SEQRES 10 C 134 TRP GLY GLN GLY THR GLN VAL THR VAL SER SER HIS HIS SEQRES 11 C 134 HIS HIS HIS HIS HET MG A 601 1 HET MG A 602 1 HET EDO A 603 4 HET MG B 601 1 HET EDO B 602 4 HET EDO B 603 4 HETNAM MG MAGNESIUM ION HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 5 MG 3(MG 2+) FORMUL 7 EDO 3(C2 H6 O2) FORMUL 11 HOH *455(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 PRO A 454 ALA A 465 1 12 HELIX 4 AA4 GLN B 236 CYS B 240 5 5 HELIX 5 AA5 SER B 282 VAL B 286 5 5 HELIX 6 AA6 ALA B 368 GLN B 371 5 4 HELIX 7 AA7 PRO B 454 ALA B 465 1 12 HELIX 8 AA8 ASP D 62 LYS D 65 5 4 HELIX 9 AA9 LYS D 87 THR D 91 5 5 HELIX 10 AB1 ARG D 111 TYR D 115 5 5 HELIX 11 AB2 ASP C 62 LYS C 65 5 4 HELIX 12 AB3 LYS C 87 THR C 91 5 5 HELIX 13 AB4 ARG C 111 TYR C 115 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 PHE A 509 -1 O PHE A 509 N LEU A 252 SHEET 1 AA2 7 PHE A 289 GLN A 298 0 SHEET 2 AA2 7 GLY A 302 ILE A 310 -1 O GLY A 302 N GLN A 298 SHEET 3 AA2 7 ARG A 373 VAL A 378 -1 O ALA A 376 N ALA A 305 SHEET 4 AA2 7 LEU A 350 GLY A 360 -1 N GLU A 356 O SER A 377 SHEET 5 AA2 7 SER A 332 GLU A 342 -1 N THR A 341 O LYS A 351 SHEET 6 AA2 7 GLY A 389 GLN A 402 -1 O GLN A 402 N SER A 332 SHEET 7 AA2 7 PHE A 289 GLN A 298 -1 N ALA A 293 O GLY A 389 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 ARG A 478 -1 N TYR A 477 O PHE A 487 SHEET 5 AA3 5 ILE A 514 VAL A 521 -1 O SER A 519 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 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 VAL B 378 -1 O VAL B 374 N PHE B 307 SHEET 4 AA5 7 LEU B 350 GLY B 360 -1 N GLU B 356 O SER B 377 SHEET 5 AA5 7 SER B 332 GLU B 342 -1 N LEU B 335 O MET B 357 SHEET 6 AA5 7 GLY B 389 GLN B 402 -1 O ARG B 396 N GLU B 336 SHEET 7 AA5 7 PHE B 289 GLN B 298 -1 N ALA B 293 O GLY B 389 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 D 3 GLY D 8 0 SHEET 2 AA7 4 LEU D 18 SER D 25 -1 O SER D 25 N GLN D 3 SHEET 3 AA7 4 THR D 78 LEU D 83 -1 O LEU D 81 N VAL D 20 SHEET 4 AA7 4 PHE D 68 ASP D 73 -1 N ASP D 73 O THR D 78 SHEET 1 AA8 6 GLY D 10 VAL D 12 0 SHEET 2 AA8 6 THR D 122 VAL D 126 1 O THR D 125 N GLY D 10 SHEET 3 AA8 6 ALA D 92 ALA D 98 -1 N TYR D 94 O THR D 122 SHEET 4 AA8 6 MET D 34 GLN D 39 -1 N PHE D 37 O TYR D 95 SHEET 5 AA8 6 GLU D 46 ILE D 51 -1 O VAL D 48 N TRP D 36 SHEET 6 AA8 6 THR D 58 TYR D 60 -1 O TYR D 59 N ALA D 50 SHEET 1 AA9 4 GLY D 10 VAL D 12 0 SHEET 2 AA9 4 THR D 122 VAL D 126 1 O THR D 125 N GLY D 10 SHEET 3 AA9 4 ALA D 92 ALA D 98 -1 N TYR D 94 O THR D 122 SHEET 4 AA9 4 ASP D 117 TRP D 118 -1 O ASP D 117 N ALA D 98 SHEET 1 AB1 4 GLN C 3 GLY C 8 0 SHEET 2 AB1 4 LEU C 18 SER C 25 -1 O ALA C 23 N GLN C 5 SHEET 3 AB1 4 THR C 78 LEU C 83 -1 O LEU C 81 N VAL C 20 SHEET 4 AB1 4 PHE C 68 ASP C 73 -1 N ASP C 73 O THR C 78 SHEET 1 AB2 6 LEU C 11 VAL C 12 0 SHEET 2 AB2 6 THR C 122 VAL C 126 1 O THR C 125 N VAL C 12 SHEET 3 AB2 6 ALA C 92 ALA C 98 -1 N TYR C 94 O THR C 122 SHEET 4 AB2 6 MET C 34 GLN C 39 -1 N GLN C 39 O ILE C 93 SHEET 5 AB2 6 GLU C 46 ILE C 51 -1 O ALA C 49 N TRP C 36 SHEET 6 AB2 6 THR C 58 TYR C 60 -1 O TYR C 59 N ALA C 50 SHEET 1 AB3 4 LEU C 11 VAL C 12 0 SHEET 2 AB3 4 THR C 122 VAL C 126 1 O THR C 125 N VAL C 12 SHEET 3 AB3 4 ALA C 92 ALA C 98 -1 N TYR C 94 O THR C 122 SHEET 4 AB3 4 ASP C 117 TRP C 118 -1 N ASP C 117 O ALA C 98 SSBOND 1 CYS D 22 CYS D 96 1555 1555 2.08 SSBOND 2 CYS C 22 CYS C 96 1555 1555 2.09 LINK OD2 ASP A 366 MG MG A 602 1555 1555 2.14 LINK OD1 ASP A 410 MG MG A 602 1555 1555 2.21 LINK OE1 GLN A 438 MG MG A 601 1555 1555 1.94 LINK OD2 ASP A 440 MG MG A 601 1555 1555 1.98 LINK MG MG A 601 O HOH A 708 1555 1555 2.00 LINK MG MG A 601 O HOH A 728 1555 1555 1.90 LINK MG MG A 601 O HOH A 802 1555 1555 2.12 LINK MG MG A 601 O HOH A 826 1555 1555 2.15 LINK MG MG A 602 O HOH A 709 1555 1555 2.30 LINK MG MG A 602 O HOH A 807 1555 1555 2.19 LINK MG MG A 602 O HOH A 852 1555 1555 2.35 LINK MG MG A 602 O HOH A 860 1555 1555 2.19 LINK OE1 GLN B 438 MG MG B 601 1555 1555 1.89 LINK OD2 ASP B 440 MG MG B 601 1555 1555 2.31 LINK MG MG B 601 O HOH B 722 1555 1555 2.27 LINK MG MG B 601 O HOH B 777 1555 1555 1.92 LINK MG MG B 601 O HOH B 816 1555 1555 2.22 LINK MG MG B 601 O HOH B 835 1555 1555 2.18 CISPEP 1 GLY A 360 PRO A 361 0 9.19 CISPEP 2 GLY A 421 PRO A 422 0 -0.12 CISPEP 3 GLY B 360 PRO B 361 0 11.17 CISPEP 4 GLY B 421 PRO B 422 0 7.03 SITE 1 AC1 6 GLN A 438 ASP A 440 HOH A 708 HOH A 728 SITE 2 AC1 6 HOH A 802 HOH A 826 SITE 1 AC2 6 ASP A 366 ASP A 410 HOH A 709 HOH A 807 SITE 2 AC2 6 HOH A 852 HOH A 860 SITE 1 AC3 5 LEU A 258 ASP A 403 ALA A 448 ILE A 449 SITE 2 AC3 5 ASP A 450 SITE 1 AC4 6 GLN B 438 ASP B 440 HOH B 722 HOH B 777 SITE 2 AC4 6 HOH B 816 HOH B 835 SITE 1 AC5 6 LEU B 258 ASP B 403 ARG B 433 ALA B 448 SITE 2 AC5 6 ILE B 449 ASP B 450 SITE 1 AC6 2 GLU B 311 ASP B 313 CRYST1 72.690 85.290 77.970 90.00 113.47 90.00 P 1 21 1 4 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 0.013757 0.000000 0.005973 0.00000 SCALE2 0.000000 0.011725 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013982 0.00000