HEADER IMMUNE SYSTEM 24-OCT-16 5M6A TITLE CRYSTAL STRUCTURE OF CARDIOTOXIC BENCE-JONES LIGHT CHAIN DIMER H9 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BENCE-JONES LIGHT CHAIN; COMPND 3 CHAIN: A, B, C, D SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS LIGHT CHAIN DIMER, LIGHT CHAIN AMYLOIDOSIS, IMMUNOGLOBULIN FOLD, KEYWDS 2 PROTEIN AGGREGATION, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR L.OBERTI,P.ROGNONI,J.BACARIZO,M.BOLOGNESI,S.RICAGNO REVDAT 3 17-JAN-24 5M6A 1 REMARK REVDAT 2 13-DEC-17 5M6A 1 JRNL REVDAT 1 15-NOV-17 5M6A 0 JRNL AUTH L.OBERTI,P.ROGNONI,A.BARBIROLI,F.LAVATELLI,R.RUSSO, JRNL AUTH 2 M.MARITAN,G.PALLADINI,M.BOLOGNESI,G.MERLINI,S.RICAGNO JRNL TITL CONCURRENT STRUCTURAL AND BIOPHYSICAL TRAITS LINK WITH JRNL TITL 2 IMMUNOGLOBULIN LIGHT CHAINS AMYLOID PROPENSITY. JRNL REF SCI REP V. 7 16809 2017 JRNL REFN ESSN 2045-2322 JRNL PMID 29196671 JRNL DOI 10.1038/S41598-017-16953-7 REMARK 2 REMARK 2 RESOLUTION. 1.64 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.10.3 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.64 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 45.77 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 3 NUMBER OF REFLECTIONS : 113747 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) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.183 REMARK 3 FREE R VALUE : 0.203 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 5715 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 1.64 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 1.68 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.08 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 8263 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.2195 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 7857 REMARK 3 BIN R VALUE (WORKING SET) : 0.2172 REMARK 3 BIN FREE R VALUE : 0.2649 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 4.91 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 406 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6246 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 39 REMARK 3 SOLVENT ATOMS : 882 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 22.59 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.75 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.17560 REMARK 3 B22 (A**2) : 0.01020 REMARK 3 B33 (A**2) : -0.18580 REMARK 3 B12 (A**2) : -0.15790 REMARK 3 B13 (A**2) : 0.49020 REMARK 3 B23 (A**2) : -0.22280 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.210 REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.094 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.088 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.090 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.086 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.955 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 6663 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 9138 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 2164 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 140 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 1000 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 6663 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 897 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 8286 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.14 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 4.04 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 15.06 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: { A|* } REMARK 3 ORIGIN FOR THE GROUP (A): 19.5968 0.0974 5.8651 REMARK 3 T TENSOR REMARK 3 T11: -0.0159 T22: -0.0324 REMARK 3 T33: -0.0102 T12: 0.0317 REMARK 3 T13: 0.0119 T23: 0.0216 REMARK 3 L TENSOR REMARK 3 L11: 0.3039 L22: 0.1688 REMARK 3 L33: 0.8300 L12: 0.0787 REMARK 3 L13: -0.2710 L23: 0.3687 REMARK 3 S TENSOR REMARK 3 S11: 0.0765 S12: -0.0390 S13: -0.0205 REMARK 3 S21: -0.0167 S22: -0.0550 S23: 0.0189 REMARK 3 S31: -0.0701 S32: -0.0909 S33: -0.0214 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: { B|* } REMARK 3 ORIGIN FOR THE GROUP (A): 34.3905 -5.7179 8.7551 REMARK 3 T TENSOR REMARK 3 T11: -0.0412 T22: -0.0165 REMARK 3 T33: -0.0373 T12: 0.0230 REMARK 3 T13: -0.0124 T23: 0.0055 REMARK 3 L TENSOR REMARK 3 L11: 0.1612 L22: 0.3359 REMARK 3 L33: 1.8865 L12: 0.0221 REMARK 3 L13: -0.2912 L23: 0.3461 REMARK 3 S TENSOR REMARK 3 S11: 0.0570 S12: -0.0171 S13: 0.0348 REMARK 3 S21: 0.0101 S22: 0.0020 S23: -0.0343 REMARK 3 S31: 0.0541 S32: -0.0058 S33: -0.0590 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: { C|* } REMARK 3 ORIGIN FOR THE GROUP (A): 35.8647 26.7579 -32.5617 REMARK 3 T TENSOR REMARK 3 T11: -0.0032 T22: -0.0621 REMARK 3 T33: -0.0544 T12: -0.0186 REMARK 3 T13: 0.0107 T23: -0.0263 REMARK 3 L TENSOR REMARK 3 L11: 0.2069 L22: 0.4920 REMARK 3 L33: 1.4179 L12: 0.0281 REMARK 3 L13: -0.1144 L23: -0.1260 REMARK 3 S TENSOR REMARK 3 S11: 0.0100 S12: 0.0245 S13: -0.0030 REMARK 3 S21: 0.0635 S22: 0.0065 S23: 0.0544 REMARK 3 S31: 0.0722 S32: -0.0227 S33: -0.0165 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 SELECTION: { D|* } REMARK 3 ORIGIN FOR THE GROUP (A): 47.9573 38.0187 -29.9827 REMARK 3 T TENSOR REMARK 3 T11: -0.0384 T22: -0.0832 REMARK 3 T33: -0.0148 T12: 0.0176 REMARK 3 T13: 0.0459 T23: -0.0270 REMARK 3 L TENSOR REMARK 3 L11: 0.3941 L22: 0.7359 REMARK 3 L33: 1.7310 L12: 0.3557 REMARK 3 L13: -0.2689 L23: -0.7018 REMARK 3 S TENSOR REMARK 3 S11: -0.0162 S12: 0.0520 S13: -0.1294 REMARK 3 S21: 0.0375 S22: -0.0821 S23: -0.1027 REMARK 3 S31: 0.0760 S32: 0.1772 S33: 0.0983 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5M6A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 24-OCT-16. REMARK 100 THE DEPOSITION ID IS D_1200002006. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-NOV-15 REMARK 200 TEMPERATURE (KELVIN) : 110 REMARK 200 PH : 5.5 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) : 0.979 REMARK 200 MONOCHROMATOR : SI(111) AND SI(311) LIQUID REMARK 200 NITROGEN COOLED CHANNEL-CUT REMARK 200 SILICON MONOCHROMATOR 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 : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 113757 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.640 REMARK 200 RESOLUTION RANGE LOW (A) : 45.770 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.7 REMARK 200 DATA REDUNDANCY : 3.600 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.64 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.70 REMARK 200 COMPLETENESS FOR SHELL (%) : 94.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.70 REMARK 200 R MERGE FOR SHELL (I) : 0.54000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.600 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: 1JVK REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.85 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE, 16 % W/V PEG REMARK 280 4000, 10 % V/V 2-PROPANOL, PH 5.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3930 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19610 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -37.0 KCAL/MOL 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3940 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19200 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -28.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 ASP A 96 REMARK 465 GLN B 1 REMARK 465 SER B 216 REMARK 465 GLN C 1 REMARK 465 SER C 2 REMARK 465 GLU C 214 REMARK 465 CYS C 215 REMARK 465 SER C 216 REMARK 465 THR D 213 REMARK 465 GLU D 214 REMARK 465 CYS D 215 REMARK 465 SER D 216 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 D 1 CG CD OE1 NE2 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 LYS A 160 CG CD CE NZ REMARK 480 GLU A 214 CG CD OE1 OE2 REMARK 480 ASN D 97 CG OD1 ND2 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 28 -92.84 -120.69 REMARK 500 ASP A 33 68.93 -105.89 REMARK 500 VAL A 53 -51.07 73.53 REMARK 500 ASP A 155 -115.30 63.66 REMARK 500 ASP A 155 -115.49 63.66 REMARK 500 ASP B 28 -92.65 -128.33 REMARK 500 ASP B 33 56.76 -104.50 REMARK 500 VAL B 53 -49.25 72.99 REMARK 500 ASN B 62 3.59 -68.59 REMARK 500 ALA B 134 48.35 -143.46 REMARK 500 ASP B 155 -127.32 59.11 REMARK 500 ASP C 28 -93.59 -122.53 REMARK 500 ASP C 33 44.85 -100.17 REMARK 500 VAL C 53 -49.42 71.36 REMARK 500 ASN C 62 0.83 -69.21 REMARK 500 ASN C 97 13.61 58.34 REMARK 500 ASP C 155 -121.07 57.39 REMARK 500 ASP D 28 -88.01 -120.98 REMARK 500 ASP D 33 64.96 -103.83 REMARK 500 VAL D 53 -51.19 76.00 REMARK 500 ASP D 96 -156.68 -88.84 REMARK 500 ASP D 155 -114.06 63.00 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 GOL A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL C 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL D 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PO4 D 302 DBREF 5M6A A 1 216 PDB 5M6A 5M6A 1 216 DBREF 5M6A B 1 216 PDB 5M6A 5M6A 1 216 DBREF 5M6A C 1 216 PDB 5M6A 5M6A 1 216 DBREF 5M6A D 1 216 PDB 5M6A 5M6A 1 216 SEQRES 1 A 216 GLN SER ALA LEU THR GLN PRO PRO SER ALA SER GLY SER SEQRES 2 A 216 PRO GLY GLN SER VAL THR ILE SER CYS THR GLY THR SER SEQRES 3 A 216 SER ASP VAL GLY GLY SER ASP SER VAL SER TRP TYR GLN SEQRES 4 A 216 GLN HIS PRO GLY LYS ALA PRO LYS LEU ILE ILE TYR GLU SEQRES 5 A 216 VAL SER GLN ARG PRO SER GLY VAL PRO ASN ARG PHE SER SEQRES 6 A 216 GLY SER LYS SER GLY ASN THR ALA SER LEU THR VAL SER SEQRES 7 A 216 GLY LEU GLN ALA GLU ASP ASP ALA ASP TYR TYR CYS SER SEQRES 8 A 216 SER TYR GLY GLY ASP ASN ASN LEU PHE PHE GLY GLY GLY SEQRES 9 A 216 THR LYS VAL THR VAL LEU GLY GLN PRO LYS ALA ALA PRO SEQRES 10 A 216 SER VAL THR LEU PHE PRO PRO SER SER GLU GLU LEU GLN SEQRES 11 A 216 ALA ASN LYS ALA THR LEU VAL CYS LEU ILE SER ASP PHE SEQRES 12 A 216 TYR PRO GLY ALA VAL THR VAL ALA TRP LYS ALA ASP SER SEQRES 13 A 216 SER PRO VAL LYS ALA GLY VAL GLU THR THR THR PRO SER SEQRES 14 A 216 LYS GLN SER ASN ASN LYS TYR ALA ALA SER SER TYR LEU SEQRES 15 A 216 SER LEU THR PRO GLU GLN TRP LYS SER HIS ARG SER TYR SEQRES 16 A 216 SER CYS GLN VAL THR HIS GLU GLY SER THR VAL GLU LYS SEQRES 17 A 216 THR VAL ALA PRO THR GLU CYS SER SEQRES 1 B 216 GLN SER ALA LEU THR GLN PRO PRO SER ALA SER GLY SER SEQRES 2 B 216 PRO GLY GLN SER VAL THR ILE SER CYS THR GLY THR SER SEQRES 3 B 216 SER ASP VAL GLY GLY SER ASP SER VAL SER TRP TYR GLN SEQRES 4 B 216 GLN HIS PRO GLY LYS ALA PRO LYS LEU ILE ILE TYR GLU SEQRES 5 B 216 VAL SER GLN ARG PRO SER GLY VAL PRO ASN ARG PHE SER SEQRES 6 B 216 GLY SER LYS SER GLY ASN THR ALA SER LEU THR VAL SER SEQRES 7 B 216 GLY LEU GLN ALA GLU ASP ASP ALA ASP TYR TYR CYS SER SEQRES 8 B 216 SER TYR GLY GLY ASP ASN ASN LEU PHE PHE GLY GLY GLY SEQRES 9 B 216 THR LYS VAL THR VAL LEU GLY GLN PRO LYS ALA ALA PRO SEQRES 10 B 216 SER VAL THR LEU PHE PRO PRO SER SER GLU GLU LEU GLN SEQRES 11 B 216 ALA ASN LYS ALA THR LEU VAL CYS LEU ILE SER ASP PHE SEQRES 12 B 216 TYR PRO GLY ALA VAL THR VAL ALA TRP LYS ALA ASP SER SEQRES 13 B 216 SER PRO VAL LYS ALA GLY VAL GLU THR THR THR PRO SER SEQRES 14 B 216 LYS GLN SER ASN ASN LYS TYR ALA ALA SER SER TYR LEU SEQRES 15 B 216 SER LEU THR PRO GLU GLN TRP LYS SER HIS ARG SER TYR SEQRES 16 B 216 SER CYS GLN VAL THR HIS GLU GLY SER THR VAL GLU LYS SEQRES 17 B 216 THR VAL ALA PRO THR GLU CYS SER SEQRES 1 C 216 GLN SER ALA LEU THR GLN PRO PRO SER ALA SER GLY SER SEQRES 2 C 216 PRO GLY GLN SER VAL THR ILE SER CYS THR GLY THR SER SEQRES 3 C 216 SER ASP VAL GLY GLY SER ASP SER VAL SER TRP TYR GLN SEQRES 4 C 216 GLN HIS PRO GLY LYS ALA PRO LYS LEU ILE ILE TYR GLU SEQRES 5 C 216 VAL SER GLN ARG PRO SER GLY VAL PRO ASN ARG PHE SER SEQRES 6 C 216 GLY SER LYS SER GLY ASN THR ALA SER LEU THR VAL SER SEQRES 7 C 216 GLY LEU GLN ALA GLU ASP ASP ALA ASP TYR TYR CYS SER SEQRES 8 C 216 SER TYR GLY GLY ASP ASN ASN LEU PHE PHE GLY GLY GLY SEQRES 9 C 216 THR LYS VAL THR VAL LEU GLY GLN PRO LYS ALA ALA PRO SEQRES 10 C 216 SER VAL THR LEU PHE PRO PRO SER SER GLU GLU LEU GLN SEQRES 11 C 216 ALA ASN LYS ALA THR LEU VAL CYS LEU ILE SER ASP PHE SEQRES 12 C 216 TYR PRO GLY ALA VAL THR VAL ALA TRP LYS ALA ASP SER SEQRES 13 C 216 SER PRO VAL LYS ALA GLY VAL GLU THR THR THR PRO SER SEQRES 14 C 216 LYS GLN SER ASN ASN LYS TYR ALA ALA SER SER TYR LEU SEQRES 15 C 216 SER LEU THR PRO GLU GLN TRP LYS SER HIS ARG SER TYR SEQRES 16 C 216 SER CYS GLN VAL THR HIS GLU GLY SER THR VAL GLU LYS SEQRES 17 C 216 THR VAL ALA PRO THR GLU CYS SER SEQRES 1 D 216 GLN SER ALA LEU THR GLN PRO PRO SER ALA SER GLY SER SEQRES 2 D 216 PRO GLY GLN SER VAL THR ILE SER CYS THR GLY THR SER SEQRES 3 D 216 SER ASP VAL GLY GLY SER ASP SER VAL SER TRP TYR GLN SEQRES 4 D 216 GLN HIS PRO GLY LYS ALA PRO LYS LEU ILE ILE TYR GLU SEQRES 5 D 216 VAL SER GLN ARG PRO SER GLY VAL PRO ASN ARG PHE SER SEQRES 6 D 216 GLY SER LYS SER GLY ASN THR ALA SER LEU THR VAL SER SEQRES 7 D 216 GLY LEU GLN ALA GLU ASP ASP ALA ASP TYR TYR CYS SER SEQRES 8 D 216 SER TYR GLY GLY ASP ASN ASN LEU PHE PHE GLY GLY GLY SEQRES 9 D 216 THR LYS VAL THR VAL LEU GLY GLN PRO LYS ALA ALA PRO SEQRES 10 D 216 SER VAL THR LEU PHE PRO PRO SER SER GLU GLU LEU GLN SEQRES 11 D 216 ALA ASN LYS ALA THR LEU VAL CYS LEU ILE SER ASP PHE SEQRES 12 D 216 TYR PRO GLY ALA VAL THR VAL ALA TRP LYS ALA ASP SER SEQRES 13 D 216 SER PRO VAL LYS ALA GLY VAL GLU THR THR THR PRO SER SEQRES 14 D 216 LYS GLN SER ASN ASN LYS TYR ALA ALA SER SER TYR LEU SEQRES 15 D 216 SER LEU THR PRO GLU GLN TRP LYS SER HIS ARG SER TYR SEQRES 16 D 216 SER CYS GLN VAL THR HIS GLU GLY SER THR VAL GLU LYS SEQRES 17 D 216 THR VAL ALA PRO THR GLU CYS SER HET GOL A 301 6 HET PO4 A 302 5 HET GOL B 301 6 HET PO4 B 302 5 HET GOL C 301 6 HET GOL D 301 6 HET PO4 D 302 5 HETNAM GOL GLYCEROL HETNAM PO4 PHOSPHATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 5 GOL 4(C3 H8 O3) FORMUL 6 PO4 3(O4 P 3-) FORMUL 12 HOH *882(H2 O) HELIX 1 AA1 ASP A 28 SER A 32 5 5 HELIX 2 AA2 GLN A 81 ASP A 85 5 5 HELIX 3 AA3 SER A 125 ALA A 131 1 7 HELIX 4 AA4 THR A 185 HIS A 192 1 8 HELIX 5 AA5 ASP B 28 SER B 32 5 5 HELIX 6 AA6 GLN B 81 ASP B 85 5 5 HELIX 7 AA7 SER B 125 ALA B 131 1 7 HELIX 8 AA8 THR B 185 HIS B 192 1 8 HELIX 9 AA9 ASP C 28 SER C 32 5 5 HELIX 10 AB1 GLN C 81 ASP C 85 5 5 HELIX 11 AB2 SER C 125 ALA C 131 1 7 HELIX 12 AB3 THR C 185 HIS C 192 1 8 HELIX 13 AB4 ASP D 28 SER D 32 5 5 HELIX 14 AB5 GLN D 81 ASP D 85 5 5 HELIX 15 AB6 GLU D 127 ASN D 132 5 6 HELIX 16 AB7 THR D 185 HIS D 192 1 8 SHEET 1 AA1 5 SER A 9 GLY A 12 0 SHEET 2 AA1 5 THR A 105 VAL A 109 1 O THR A 108 N ALA A 10 SHEET 3 AA1 5 ALA A 86 TYR A 93 -1 N ALA A 86 O VAL A 107 SHEET 4 AA1 5 SER A 36 GLN A 40 -1 N GLN A 40 O ASP A 87 SHEET 5 AA1 5 LYS A 47 ILE A 50 -1 O ILE A 49 N TRP A 37 SHEET 1 AA2 4 SER A 9 GLY A 12 0 SHEET 2 AA2 4 THR A 105 VAL A 109 1 O THR A 108 N ALA A 10 SHEET 3 AA2 4 ALA A 86 TYR A 93 -1 N ALA A 86 O VAL A 107 SHEET 4 AA2 4 LEU A 99 PHE A 101 -1 O PHE A 100 N SER A 92 SHEET 1 AA3 3 VAL A 18 THR A 23 0 SHEET 2 AA3 3 THR A 72 VAL A 77 -1 O VAL A 77 N VAL A 18 SHEET 3 AA3 3 PHE A 64 SER A 69 -1 N SER A 65 O THR A 76 SHEET 1 AA4 4 SER A 118 PHE A 122 0 SHEET 2 AA4 4 LEU A 136 PHE A 143 -1 O LEU A 139 N THR A 120 SHEET 3 AA4 4 TYR A 176 LEU A 182 -1 O SER A 180 N CYS A 138 SHEET 4 AA4 4 VAL A 163 THR A 165 -1 N GLU A 164 O TYR A 181 SHEET 1 AA5 4 SER A 118 PHE A 122 0 SHEET 2 AA5 4 LEU A 136 PHE A 143 -1 O LEU A 139 N THR A 120 SHEET 3 AA5 4 TYR A 176 LEU A 182 -1 O SER A 180 N CYS A 138 SHEET 4 AA5 4 SER A 169 LYS A 170 -1 N SER A 169 O ALA A 177 SHEET 1 AA6 4 SER A 157 VAL A 159 0 SHEET 2 AA6 4 THR A 149 ALA A 154 -1 N ALA A 154 O SER A 157 SHEET 3 AA6 4 TYR A 195 HIS A 201 -1 O GLN A 198 N ALA A 151 SHEET 4 AA6 4 SER A 204 VAL A 210 -1 O VAL A 206 N VAL A 199 SHEET 1 AA7 5 SER B 9 GLY B 12 0 SHEET 2 AA7 5 THR B 105 VAL B 109 1 O THR B 108 N ALA B 10 SHEET 3 AA7 5 ALA B 86 TYR B 93 -1 N ALA B 86 O VAL B 107 SHEET 4 AA7 5 SER B 36 GLN B 40 -1 N GLN B 40 O ASP B 87 SHEET 5 AA7 5 LYS B 47 ILE B 50 -1 O LYS B 47 N GLN B 39 SHEET 1 AA8 4 SER B 9 GLY B 12 0 SHEET 2 AA8 4 THR B 105 VAL B 109 1 O THR B 108 N ALA B 10 SHEET 3 AA8 4 ALA B 86 TYR B 93 -1 N ALA B 86 O VAL B 107 SHEET 4 AA8 4 LEU B 99 PHE B 101 -1 O PHE B 100 N SER B 92 SHEET 1 AA9 3 VAL B 18 THR B 23 0 SHEET 2 AA9 3 THR B 72 VAL B 77 -1 O VAL B 77 N VAL B 18 SHEET 3 AA9 3 PHE B 64 SER B 69 -1 N SER B 65 O THR B 76 SHEET 1 AB1 4 SER B 118 PHE B 122 0 SHEET 2 AB1 4 LEU B 136 PHE B 143 -1 O LEU B 139 N THR B 120 SHEET 3 AB1 4 TYR B 176 LEU B 182 -1 O SER B 180 N CYS B 138 SHEET 4 AB1 4 VAL B 163 THR B 165 -1 N GLU B 164 O TYR B 181 SHEET 1 AB2 4 SER B 118 PHE B 122 0 SHEET 2 AB2 4 LEU B 136 PHE B 143 -1 O LEU B 139 N THR B 120 SHEET 3 AB2 4 TYR B 176 LEU B 182 -1 O SER B 180 N CYS B 138 SHEET 4 AB2 4 SER B 169 LYS B 170 -1 N SER B 169 O ALA B 177 SHEET 1 AB3 4 SER B 157 PRO B 158 0 SHEET 2 AB3 4 THR B 149 ALA B 154 -1 N ALA B 154 O SER B 157 SHEET 3 AB3 4 TYR B 195 HIS B 201 -1 O GLN B 198 N ALA B 151 SHEET 4 AB3 4 SER B 204 VAL B 210 -1 O VAL B 206 N VAL B 199 SHEET 1 AB4 5 SER C 9 GLY C 12 0 SHEET 2 AB4 5 THR C 105 VAL C 109 1 O THR C 108 N ALA C 10 SHEET 3 AB4 5 ALA C 86 TYR C 93 -1 N ALA C 86 O VAL C 107 SHEET 4 AB4 5 SER C 36 GLN C 40 -1 N GLN C 40 O ASP C 87 SHEET 5 AB4 5 LYS C 47 ILE C 50 -1 O LYS C 47 N GLN C 39 SHEET 1 AB5 4 SER C 9 GLY C 12 0 SHEET 2 AB5 4 THR C 105 VAL C 109 1 O THR C 108 N ALA C 10 SHEET 3 AB5 4 ALA C 86 TYR C 93 -1 N ALA C 86 O VAL C 107 SHEET 4 AB5 4 LEU C 99 PHE C 101 -1 O PHE C 100 N SER C 92 SHEET 1 AB6 3 VAL C 18 THR C 23 0 SHEET 2 AB6 3 THR C 72 VAL C 77 -1 O LEU C 75 N ILE C 20 SHEET 3 AB6 3 PHE C 64 SER C 69 -1 N SER C 65 O THR C 76 SHEET 1 AB7 4 SER C 118 PHE C 122 0 SHEET 2 AB7 4 ALA C 134 PHE C 143 -1 O LEU C 139 N THR C 120 SHEET 3 AB7 4 TYR C 176 LEU C 184 -1 O TYR C 176 N PHE C 143 SHEET 4 AB7 4 VAL C 163 THR C 165 -1 N GLU C 164 O TYR C 181 SHEET 1 AB8 4 SER C 118 PHE C 122 0 SHEET 2 AB8 4 ALA C 134 PHE C 143 -1 O LEU C 139 N THR C 120 SHEET 3 AB8 4 TYR C 176 LEU C 184 -1 O TYR C 176 N PHE C 143 SHEET 4 AB8 4 SER C 169 LYS C 170 -1 N SER C 169 O ALA C 177 SHEET 1 AB9 4 SER C 157 VAL C 159 0 SHEET 2 AB9 4 THR C 149 ALA C 154 -1 N ALA C 154 O SER C 157 SHEET 3 AB9 4 TYR C 195 HIS C 201 -1 O GLN C 198 N ALA C 151 SHEET 4 AB9 4 SER C 204 VAL C 210 -1 O VAL C 206 N VAL C 199 SHEET 1 AC1 5 SER D 9 GLY D 12 0 SHEET 2 AC1 5 THR D 105 VAL D 109 1 O THR D 108 N ALA D 10 SHEET 3 AC1 5 ALA D 86 TYR D 93 -1 N ALA D 86 O VAL D 107 SHEET 4 AC1 5 SER D 36 GLN D 40 -1 N GLN D 40 O ASP D 87 SHEET 5 AC1 5 LYS D 47 ILE D 50 -1 O ILE D 49 N TRP D 37 SHEET 1 AC2 4 SER D 9 GLY D 12 0 SHEET 2 AC2 4 THR D 105 VAL D 109 1 O THR D 108 N ALA D 10 SHEET 3 AC2 4 ALA D 86 TYR D 93 -1 N ALA D 86 O VAL D 107 SHEET 4 AC2 4 LEU D 99 PHE D 101 -1 O PHE D 100 N SER D 92 SHEET 1 AC3 3 VAL D 18 THR D 23 0 SHEET 2 AC3 3 THR D 72 VAL D 77 -1 O ALA D 73 N CYS D 22 SHEET 3 AC3 3 PHE D 64 SER D 69 -1 N SER D 67 O SER D 74 SHEET 1 AC4 4 SER D 118 PHE D 122 0 SHEET 2 AC4 4 LEU D 136 PHE D 143 -1 O VAL D 137 N PHE D 122 SHEET 3 AC4 4 TYR D 176 LEU D 182 -1 O ALA D 178 N ILE D 140 SHEET 4 AC4 4 VAL D 163 THR D 165 -1 N GLU D 164 O TYR D 181 SHEET 1 AC5 4 SER D 118 PHE D 122 0 SHEET 2 AC5 4 LEU D 136 PHE D 143 -1 O VAL D 137 N PHE D 122 SHEET 3 AC5 4 TYR D 176 LEU D 182 -1 O ALA D 178 N ILE D 140 SHEET 4 AC5 4 SER D 169 LYS D 170 -1 N SER D 169 O ALA D 177 SHEET 1 AC6 4 SER D 157 VAL D 159 0 SHEET 2 AC6 4 THR D 149 ALA D 154 -1 N ALA D 154 O SER D 157 SHEET 3 AC6 4 TYR D 195 HIS D 201 -1 O GLN D 198 N ALA D 151 SHEET 4 AC6 4 SER D 204 VAL D 210 -1 O VAL D 206 N VAL D 199 SSBOND 1 CYS A 22 CYS A 90 1555 1555 2.06 SSBOND 2 CYS A 138 CYS A 197 1555 1555 2.03 SSBOND 3 CYS A 215 CYS B 215 1555 1555 2.04 SSBOND 4 CYS B 22 CYS B 90 1555 1555 2.05 SSBOND 5 CYS B 138 CYS B 197 1555 1555 2.05 SSBOND 6 CYS C 22 CYS C 90 1555 1555 2.05 SSBOND 7 CYS C 138 CYS C 197 1555 1555 2.03 SSBOND 8 CYS D 22 CYS D 90 1555 1555 2.06 SSBOND 9 CYS D 138 CYS D 197 1555 1555 2.03 CISPEP 1 TYR A 144 PRO A 145 0 -2.22 CISPEP 2 TYR B 144 PRO B 145 0 0.26 CISPEP 3 TYR C 144 PRO C 145 0 1.26 CISPEP 4 TYR D 144 PRO D 145 0 -2.04 SITE 1 AC1 5 ASN A 98 LEU A 99 HOH A 489 TYR B 51 SITE 2 AC1 5 HOH B 506 SITE 1 AC2 6 TYR A 144 TYR A 176 HOH A 406 HOH A 417 SITE 2 AC2 6 HOH A 467 ARG C 193 SITE 1 AC3 7 ARG B 193 HOH B 434 HOH B 472 TYR D 144 SITE 2 AC3 7 LYS D 170 TYR D 176 HOH D 427 SITE 1 AC4 5 TYR A 38 PRO A 46 PHE A 101 TYR B 38 SITE 2 AC4 5 PRO B 46 SITE 1 AC5 4 ALA C 3 LEU C 99 PHE C 100 HOH C 492 SITE 1 AC6 6 TYR C 51 ASN D 97 ASN D 98 LEU D 99 SITE 2 AC6 6 HOH D 416 HOH D 457 SITE 1 AC7 6 TYR C 38 PRO C 46 TYR D 38 PRO D 46 SITE 2 AC7 6 TYR D 89 PHE D 101 CRYST1 46.492 63.429 86.637 95.32 85.84 99.58 P 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 0.021509 0.003630 -0.001271 0.00000 SCALE2 0.000000 0.015989 0.001316 0.00000 SCALE3 0.000000 0.000000 0.011612 0.00000