HEADER TOXIN 22-OCT-22 8BEX TITLE STRUCTURE OF THE LYSINIBACILLUS SPHAERICUS TPP49AA1 PESTICIDAL PROTEIN TITLE 2 AT PH 3 COMPND MOL_ID: 1; COMPND 2 MOLECULE: CRY49AA PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: CRYSTAL TOXIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: LYSINIBACILLUS SPHAERICUS; SOURCE 3 ORGANISM_TAXID: 1421; SOURCE 4 GENE: CRY49AA1, CRY49AA; SOURCE 5 EXPRESSION_SYSTEM: BACILLUS THURINGIENSIS; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 1428 KEYWDS LYSINIBACILLUS SPHAERICUS, BACILLUS THURINGIENSIS, TPP49AA1, KEYWDS 2 CRY48AA1, XFEL, SFX, MOSQUITOES, CULEX QUINQUEFASCIATUS, TOXIN EXPDTA X-RAY DIFFRACTION AUTHOR L.J.WILLIAMSON,P.J.RIZKALLAH,C.BERRY,D.OBERTHUR,M.GALCHENKOVA, AUTHOR 2 O.YEFANOV,R.BEAN REVDAT 2 06-DEC-23 8BEX 1 JRNL REVDAT 1 01-NOV-23 8BEX 0 JRNL AUTH L.J.WILLIAMSON,M.GALCHENKOVA,H.L.BEST,R.J.BEAN,A.MUNKE, JRNL AUTH 2 S.AWEL,G.PENA,J.KNOSKA,R.SCHUBERT,K.DORNER,H.W.PARK, JRNL AUTH 3 D.K.BIDESHI,A.HENKEL,V.KREMLING,B.KLOPPROGGE,E.LLOYD-EVANS, JRNL AUTH 4 M.T.YOUNG,J.VALERIO,M.KLOOS,M.SIKORSKI,G.MILLS,J.BIELECKI, JRNL AUTH 5 H.KIRKWOOD,C.KIM,R.DE WIJN,K.LORENZEN,P.L.XAVIER, JRNL AUTH 6 A.RAHMANI MASHHOUR,L.GELISIO,O.YEFANOV,A.P.MANCUSO, JRNL AUTH 7 B.A.FEDERICI,H.N.CHAPMAN,N.CRICKMORE,P.J.RIZKALLAH,C.BERRY, JRNL AUTH 8 D.OBERTHUR JRNL TITL STRUCTURE OF THE LYSINIBACILLUS SPHAERICUS TPP49AA1 JRNL TITL 2 PESTICIDAL PROTEIN ELUCIDATED FROM NATURAL CRYSTALS USING JRNL TITL 3 MHZ-SFX. JRNL REF PROC.NATL.ACAD.SCI.USA V. 120 41120 2023 JRNL REFN ESSN 1091-6490 JRNL PMID 38015839 JRNL DOI 10.1073/PNAS.2203241120 REMARK 2 REMARK 2 RESOLUTION. 1.78 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 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) : 1.78 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 95333 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) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5033 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) : 1.78 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.83 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6431 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.05 REMARK 3 BIN R VALUE (WORKING SET) : 0.4400 REMARK 3 BIN FREE R VALUE SET COUNT : 386 REMARK 3 BIN FREE R VALUE : 0.4310 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6748 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 367 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 32.72 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.14000 REMARK 3 B22 (A**2) : 0.10000 REMARK 3 B33 (A**2) : 0.04000 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): 0.113 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.106 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.105 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 7.896 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.967 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7046 ; 0.011 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 6516 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 9611 ; 1.472 ; 1.648 REMARK 3 BOND ANGLES OTHERS (DEGREES): 14914 ; 1.285 ; 1.580 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 866 ; 7.566 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 457 ;34.632 ;22.057 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1161 ;13.964 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 64 ;18.105 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 927 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 8308 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1840 ; 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 NCS TYPE: LOCAL REMARK 3 NUMBER OF DIFFERENT NCS PAIRS : 1 REMARK 3 GROUP CHAIN1 RANGE CHAIN2 RANGE COUNT RMS WEIGHT REMARK 3 1 A 49 464 B 49 464 13818 0.070 0.050 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 4 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 49 A 214 REMARK 3 ORIGIN FOR THE GROUP (A): -12.2708 -24.5639 -42.3154 REMARK 3 T TENSOR REMARK 3 T11: 0.1184 T22: 0.2559 REMARK 3 T33: 0.1141 T12: 0.0524 REMARK 3 T13: -0.0531 T23: -0.1336 REMARK 3 L TENSOR REMARK 3 L11: 3.1764 L22: 3.0382 REMARK 3 L33: 3.6545 L12: -0.6010 REMARK 3 L13: 0.0964 L23: 1.2659 REMARK 3 S TENSOR REMARK 3 S11: 0.1424 S12: 0.5279 S13: -0.5196 REMARK 3 S21: -0.2271 S22: -0.2719 S23: 0.3430 REMARK 3 S31: 0.1696 S32: -0.1552 S33: 0.1296 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 215 A 463 REMARK 3 ORIGIN FOR THE GROUP (A): -3.7308 1.4857 -7.0371 REMARK 3 T TENSOR REMARK 3 T11: 0.0893 T22: 0.1512 REMARK 3 T33: 0.0166 T12: -0.0319 REMARK 3 T13: -0.0080 T23: 0.0228 REMARK 3 L TENSOR REMARK 3 L11: 0.6516 L22: 1.5130 REMARK 3 L33: 3.2101 L12: 0.3035 REMARK 3 L13: 0.4771 L23: 1.6006 REMARK 3 S TENSOR REMARK 3 S11: 0.0052 S12: -0.0859 S13: 0.0572 REMARK 3 S21: 0.0056 S22: -0.0448 S23: -0.0549 REMARK 3 S31: -0.2114 S32: 0.2383 S33: 0.0395 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 49 B 214 REMARK 3 ORIGIN FOR THE GROUP (A): -4.6167 -32.3154 2.9058 REMARK 3 T TENSOR REMARK 3 T11: 0.2200 T22: 0.2669 REMARK 3 T33: 0.1077 T12: 0.0859 REMARK 3 T13: 0.1030 T23: 0.1197 REMARK 3 L TENSOR REMARK 3 L11: 2.8964 L22: 2.6825 REMARK 3 L33: 4.4856 L12: -0.5300 REMARK 3 L13: -1.1679 L23: -0.6107 REMARK 3 S TENSOR REMARK 3 S11: -0.1673 S12: -0.3432 S13: -0.3388 REMARK 3 S21: 0.4314 S22: 0.2357 S23: 0.4289 REMARK 3 S31: 0.0191 S32: -0.3433 S33: -0.0684 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 215 B 463 REMARK 3 ORIGIN FOR THE GROUP (A): 21.4709 -24.7310 -32.5325 REMARK 3 T TENSOR REMARK 3 T11: 0.1070 T22: 0.1125 REMARK 3 T33: 0.0136 T12: -0.0245 REMARK 3 T13: -0.0191 T23: 0.0060 REMARK 3 L TENSOR REMARK 3 L11: 1.8704 L22: 0.5888 REMARK 3 L33: 3.1105 L12: 0.3099 REMARK 3 L13: -1.5487 L23: -0.4185 REMARK 3 S TENSOR REMARK 3 S11: -0.0404 S12: 0.0290 S13: 0.0807 REMARK 3 S21: -0.0516 S22: 0.0377 S23: -0.0397 REMARK 3 S31: -0.2261 S32: 0.1935 S33: 0.0027 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 : WITH TLS ADDED REMARK 4 REMARK 4 8BEX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 22-OCT-22. REMARK 100 THE DEPOSITION ID IS D_1292124984. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-22 REMARK 200 TEMPERATURE (KELVIN) : 298 REMARK 200 PH : 3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : FREE ELECTRON LASER REMARK 200 BEAMLINE : SPB/SFX REMARK 200 X-RAY GENERATOR MODEL : EUROPEAN XFEL BEAMLINE SPB/SFX REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.33 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : AGIPD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : CRYSTFEL REMARK 200 DATA SCALING SOFTWARE : CRYSTFEL AMBIGATOR REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 100541 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.780 REMARK 200 RESOLUTION RANGE LOW (A) : 36.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 183.7 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.78 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 92.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.8.3 REMARK 200 STARTING MODEL: 3WA1, 5FOY, 5G37 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.97 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.73 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NATURALLY GROWN, PH 3, IN CELL, REMARK 280 TEMPERATURE 298K 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 39.94500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 78.94000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.42000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 78.94000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 39.94500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.42000 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 OD1 ASN B 357 O HOH B 501 1.85 REMARK 500 OD1 ASN B 69 O HOH B 502 1.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O ASP A 429 NH2 ARG B 267 4445 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ASN A 309 CB - CA - C ANGL. DEV. = 13.0 DEGREES REMARK 500 ASN B 309 CB - CA - C ANGL. DEV. = 13.3 DEGREES REMARK 500 ARG B 331 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 ARG B 331 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: TORSION ANGLES REMARK 500 REMARK 500 TORSION ANGLES OUTSIDE THE EXPECTED RAMACHANDRAN REGIONS: REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT:(10X,I3,1X,A3,1X,A1,I4,A1,4X,F7.2,3X,F7.2) REMARK 500 REMARK 500 EXPECTED VALUES: GJ KLEYWEGT AND TA JONES (1996). PHI/PSI- REMARK 500 CHOLOGY: RAMACHANDRAN REVISITED. STRUCTURE 4, 1395 - 1400 REMARK 500 REMARK 500 M RES CSSEQI PSI PHI REMARK 500 ASN A 51 51.06 -97.02 REMARK 500 ASN A 76 50.65 -111.82 REMARK 500 SER A 275 62.51 -154.26 REMARK 500 ASN B 51 52.39 -95.91 REMARK 500 GLN B 152 -60.92 -96.60 REMARK 500 ASP B 175 -17.20 87.28 REMARK 500 SER B 275 62.47 -154.65 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 7QA1 RELATED DB: PDB REMARK 900 LOWER RESOLUTION DBREF 8BEX A 49 464 UNP A7WK53 A7WK53_LYSSH 49 464 DBREF 8BEX B 49 464 UNP A7WK53 A7WK53_LYSSH 49 464 SEQRES 1 A 416 ASN LEU ASN LEU PRO GLU GLN SER THR ARG PHE GLN THR SEQRES 2 A 416 ILE ALA SER ILE HIS SER ASN ASN CYS SER PHE GLU ILE SEQRES 3 A 416 LEU ASN ASN ASP PRO GLY TYR ILE TYR GLY ASP SER VAL SEQRES 4 A 416 ASP GLY GLU CYS ARG ILE ALA VAL ALA HIS ARG GLU LEU SEQRES 5 A 416 GLY ASN GLY LEU GLU ARG THR GLY ASP ASP ARG PHE LEU SEQRES 6 A 416 PHE ILE PHE TYR ALA LEU ASP ASN ASN ASN PHE ILE ILE SEQRES 7 A 416 ALA ASN ARG HIS ASP GLY PHE VAL LEU GLN PHE LEU ILE SEQRES 8 A 416 ALA ASN GLY GLN GLY VAL ILE VAL SER ARG GLU TYR GLN SEQRES 9 A 416 PRO ASN ILE HIS GLN GLU PHE THR ILE GLN SER ILE ASN SEQRES 10 A 416 SER ASP THR PHE ARG LEU HIS SER ARG ASP THR ASN THR SEQRES 11 A 416 PHE ALA THR VAL CYS TRP ALA GLN PHE ASN SER TRP THR SEQRES 12 A 416 LYS ILE VAL SER ARG VAL ASP ASN PRO GLY ALA PRO ASN SEQRES 13 A 416 ALA ASN LEU LYS HIS ARG SER LEU LEU THR ASP ILE ASN SEQRES 14 A 416 MET PRO GLN LEU PRO SER LEU THR PRO LEU GLN PRO LEU SEQRES 15 A 416 PRO ARG LEU THR GLU LEU GLU ASP GLY GLY LEU SER PRO SEQRES 16 A 416 ALA GLN ALA PRO ARG ALA ILE ILE GLY ARG THR LEU ILE SEQRES 17 A 416 PRO CYS LEU PHE VAL ASN ASP PRO VAL LEU ARG LEU GLU SEQRES 18 A 416 ASN ARG ILE LYS GLN SER PRO TYR TYR VAL LEU GLU HIS SEQRES 19 A 416 ARG GLN TYR TRP HIS ARG ILE TRP THR ASP ILE PHE THR SEQRES 20 A 416 ALA GLY GLU ARG ARG GLU TYR ARG GLU VAL THR GLY ILE SEQRES 21 A 416 ASN ASN ASN ALA GLN ASN ASP MET ASN LYS MET ILE ASN SEQRES 22 A 416 ILE THR ILE GLY ALA ASP GLY PRO ASN ARG LEU ARG PHE SEQRES 23 A 416 GLY ASN LEU SER THR PRO PHE ARG GLN GLN ILE ILE ASP SEQRES 24 A 416 ASN SER ASN THR LEU GLY SER PHE ALA ASN THR ASN TYR SEQRES 25 A 416 GLY THR ARG THR ASP ILE VAL ASN VAL PHE ASN SER GLU SEQRES 26 A 416 PHE HIS GLN VAL ARG TYR ALA ARG PHE VAL LYS ALA TYR SEQRES 27 A 416 GLU TYR ARG LEU THR ARG ALA ASP GLY SER GLN VAL GLY SEQRES 28 A 416 THR PRO TRP VAL VAL LEU ASP ARG LYS GLU MET ASP LEU SEQRES 29 A 416 ARG THR TYR PRO HIS ASN MET ALA ILE THR LEU GLU ASN SEQRES 30 A 416 VAL LYS ILE ASP ASN ALA ASP ASN SER TYR ASP LEU SER SEQRES 31 A 416 ILE TRP LYS THR PRO LEU LYS LEU LYS ASP GLY LYS ILE SEQRES 32 A 416 ILE ILE GLU ASN HIS GLU ASN SER LYS PRO TYR TYR ASN SEQRES 1 B 416 ASN LEU ASN LEU PRO GLU GLN SER THR ARG PHE GLN THR SEQRES 2 B 416 ILE ALA SER ILE HIS SER ASN ASN CYS SER PHE GLU ILE SEQRES 3 B 416 LEU ASN ASN ASP PRO GLY TYR ILE TYR GLY ASP SER VAL SEQRES 4 B 416 ASP GLY GLU CYS ARG ILE ALA VAL ALA HIS ARG GLU LEU SEQRES 5 B 416 GLY ASN GLY LEU GLU ARG THR GLY ASP ASP ARG PHE LEU SEQRES 6 B 416 PHE ILE PHE TYR ALA LEU ASP ASN ASN ASN PHE ILE ILE SEQRES 7 B 416 ALA ASN ARG HIS ASP GLY PHE VAL LEU GLN PHE LEU ILE SEQRES 8 B 416 ALA ASN GLY GLN GLY VAL ILE VAL SER ARG GLU TYR GLN SEQRES 9 B 416 PRO ASN ILE HIS GLN GLU PHE THR ILE GLN SER ILE ASN SEQRES 10 B 416 SER ASP THR PHE ARG LEU HIS SER ARG ASP THR ASN THR SEQRES 11 B 416 PHE ALA THR VAL CYS TRP ALA GLN PHE ASN SER TRP THR SEQRES 12 B 416 LYS ILE VAL SER ARG VAL ASP ASN PRO GLY ALA PRO ASN SEQRES 13 B 416 ALA ASN LEU LYS HIS ARG SER LEU LEU THR ASP ILE ASN SEQRES 14 B 416 MET PRO GLN LEU PRO SER LEU THR PRO LEU GLN PRO LEU SEQRES 15 B 416 PRO ARG LEU THR GLU LEU GLU ASP GLY GLY LEU SER PRO SEQRES 16 B 416 ALA GLN ALA PRO ARG ALA ILE ILE GLY ARG THR LEU ILE SEQRES 17 B 416 PRO CYS LEU PHE VAL ASN ASP PRO VAL LEU ARG LEU GLU SEQRES 18 B 416 ASN ARG ILE LYS GLN SER PRO TYR TYR VAL LEU GLU HIS SEQRES 19 B 416 ARG GLN TYR TRP HIS ARG ILE TRP THR ASP ILE PHE THR SEQRES 20 B 416 ALA GLY GLU ARG ARG GLU TYR ARG GLU VAL THR GLY ILE SEQRES 21 B 416 ASN ASN ASN ALA GLN ASN ASP MET ASN LYS MET ILE ASN SEQRES 22 B 416 ILE THR ILE GLY ALA ASP GLY PRO ASN ARG LEU ARG PHE SEQRES 23 B 416 GLY ASN LEU SER THR PRO PHE ARG GLN GLN ILE ILE ASP SEQRES 24 B 416 ASN SER ASN THR LEU GLY SER PHE ALA ASN THR ASN TYR SEQRES 25 B 416 GLY THR ARG THR ASP ILE VAL ASN VAL PHE ASN SER GLU SEQRES 26 B 416 PHE HIS GLN VAL ARG TYR ALA ARG PHE VAL LYS ALA TYR SEQRES 27 B 416 GLU TYR ARG LEU THR ARG ALA ASP GLY SER GLN VAL GLY SEQRES 28 B 416 THR PRO TRP VAL VAL LEU ASP ARG LYS GLU MET ASP LEU SEQRES 29 B 416 ARG THR TYR PRO HIS ASN MET ALA ILE THR LEU GLU ASN SEQRES 30 B 416 VAL LYS ILE ASP ASN ALA ASP ASN SER TYR ASP LEU SER SEQRES 31 B 416 ILE TRP LYS THR PRO LEU LYS LEU LYS ASP GLY LYS ILE SEQRES 32 B 416 ILE ILE GLU ASN HIS GLU ASN SER LYS PRO TYR TYR ASN FORMUL 3 HOH *367(H2 O) HELIX 1 AA1 PRO A 53 THR A 57 5 5 HELIX 2 AA2 ASP A 109 PHE A 112 5 4 HELIX 3 AA3 ASN A 154 HIS A 156 5 3 HELIX 4 AA4 TRP A 184 GLN A 186 5 3 HELIX 5 AA5 LEU A 259 VAL A 261 5 3 HELIX 6 AA6 ARG A 267 SER A 275 1 9 HELIX 7 AA7 ASN A 309 ASN A 321 1 13 HELIX 8 AA8 SER A 338 PRO A 340 5 3 HELIX 9 AA9 PHE A 341 ASN A 350 1 10 HELIX 10 AB1 PRO B 53 THR B 57 5 5 HELIX 11 AB2 ASP B 109 PHE B 112 5 4 HELIX 12 AB3 ASN B 154 HIS B 156 5 3 HELIX 13 AB4 TRP B 184 GLN B 186 5 3 HELIX 14 AB5 LEU B 259 VAL B 261 5 3 HELIX 15 AB6 ARG B 267 SER B 275 1 9 HELIX 16 AB7 ASN B 309 ASN B 321 1 13 HELIX 17 AB8 SER B 338 PRO B 340 5 3 HELIX 18 AB9 PHE B 341 ASN B 350 1 10 SHEET 1 AA1 2 PHE A 59 GLN A 60 0 SHEET 2 AA1 2 LEU A 212 LEU A 213 -1 O LEU A 213 N PHE A 59 SHEET 1 AA2 2 ALA A 63 SER A 64 0 SHEET 2 AA2 2 LEU A 207 LYS A 208 -1 O LYS A 208 N ALA A 63 SHEET 1 AA3 2 CYS A 70 ILE A 74 0 SHEET 2 AA3 2 LEU A 100 LEU A 104 -1 O GLY A 103 N SER A 71 SHEET 1 AA4 6 PHE A 114 ALA A 118 0 SHEET 2 AA4 6 PHE A 124 ASN A 128 -1 O ILE A 125 N TYR A 117 SHEET 3 AA4 6 GLU A 158 ASN A 165 -1 O PHE A 159 N PHE A 124 SHEET 4 AA4 6 THR A 168 SER A 173 -1 O HIS A 172 N THR A 160 SHEET 5 AA4 6 THR A 178 VAL A 182 -1 O THR A 178 N SER A 173 SHEET 6 AA4 6 ILE A 193 ARG A 196 -1 O VAL A 194 N THR A 181 SHEET 1 AA5 2 VAL A 134 ALA A 140 0 SHEET 2 AA5 2 GLN A 143 ARG A 149 -1 O ARG A 149 N VAL A 134 SHEET 1 AA6 5 ALA A 249 PRO A 257 0 SHEET 2 AA6 5 TYR A 277 PHE A 294 -1 O GLN A 284 N ALA A 249 SHEET 3 AA6 5 VAL A 377 THR A 391 -1 O ALA A 385 N TYR A 285 SHEET 4 AA6 5 TRP A 402 TYR A 415 -1 O ASP A 406 N LYS A 384 SHEET 5 AA6 5 ILE A 452 ILE A 453 -1 O ILE A 452 N MET A 410 SHEET 1 AA7 4 ARG A 299 GLY A 307 0 SHEET 2 AA7 4 THR A 362 PHE A 370 -1 O ASP A 365 N GLU A 304 SHEET 3 AA7 4 ALA A 420 ALA A 431 -1 O ASP A 429 N THR A 364 SHEET 4 AA7 4 LEU A 444 LYS A 447 -1 O LEU A 446 N ILE A 421 SHEET 1 AA8 3 ILE A 322 ILE A 324 0 SHEET 2 AA8 3 ARG A 331 PHE A 334 -1 O ARG A 333 N THR A 323 SHEET 3 AA8 3 LEU A 352 GLY A 353 1 O LEU A 352 N LEU A 332 SHEET 1 AA9 2 SER A 438 TRP A 440 0 SHEET 2 AA9 2 SER A 459 PRO A 461 -1 O LYS A 460 N ILE A 439 SHEET 1 AB1 2 PHE B 59 GLN B 60 0 SHEET 2 AB1 2 LEU B 212 LEU B 213 -1 O LEU B 213 N PHE B 59 SHEET 1 AB2 2 ALA B 63 SER B 64 0 SHEET 2 AB2 2 LEU B 207 LYS B 208 -1 O LYS B 208 N ALA B 63 SHEET 1 AB3 2 CYS B 70 ILE B 74 0 SHEET 2 AB3 2 LEU B 100 LEU B 104 -1 O GLY B 101 N GLU B 73 SHEET 1 AB4 4 PHE B 114 ALA B 118 0 SHEET 2 AB4 4 PHE B 124 ASN B 128 -1 O ILE B 125 N TYR B 117 SHEET 3 AB4 4 GLU B 158 ASN B 165 -1 O PHE B 159 N PHE B 124 SHEET 4 AB4 4 THR B 168 SER B 173 -1 O HIS B 172 N THR B 160 SHEET 1 AB5 2 VAL B 134 ALA B 140 0 SHEET 2 AB5 2 GLN B 143 ARG B 149 -1 O ARG B 149 N VAL B 134 SHEET 1 AB6 2 PHE B 179 VAL B 182 0 SHEET 2 AB6 2 ILE B 193 ARG B 196 -1 O VAL B 194 N THR B 181 SHEET 1 AB7 5 ALA B 249 PRO B 257 0 SHEET 2 AB7 5 TYR B 277 PHE B 294 -1 O GLN B 284 N ALA B 249 SHEET 3 AB7 5 VAL B 377 THR B 391 -1 O ALA B 385 N TYR B 285 SHEET 4 AB7 5 TRP B 402 TYR B 415 -1 O ASP B 406 N LYS B 384 SHEET 5 AB7 5 ILE B 452 ILE B 453 -1 O ILE B 452 N MET B 410 SHEET 1 AB8 4 ARG B 299 GLY B 307 0 SHEET 2 AB8 4 THR B 362 PHE B 370 -1 O ASP B 365 N GLU B 304 SHEET 3 AB8 4 ALA B 420 ALA B 431 -1 O LYS B 427 N ILE B 366 SHEET 4 AB8 4 LEU B 444 LYS B 447 -1 O LEU B 446 N ILE B 421 SHEET 1 AB9 3 ILE B 322 ILE B 324 0 SHEET 2 AB9 3 ARG B 331 PHE B 334 -1 O ARG B 333 N THR B 323 SHEET 3 AB9 3 LEU B 352 GLY B 353 1 O LEU B 352 N LEU B 332 SHEET 1 AC1 2 SER B 438 TRP B 440 0 SHEET 2 AC1 2 SER B 459 PRO B 461 -1 O LYS B 460 N ILE B 439 SSBOND 1 CYS A 91 CYS A 183 1555 1555 2.05 SSBOND 2 CYS B 91 CYS B 183 1555 1555 2.04 CISPEP 1 GLN A 152 PRO A 153 0 -8.21 CISPEP 2 TYR A 415 PRO A 416 0 -2.49 CISPEP 3 THR A 442 PRO A 443 0 -4.55 CISPEP 4 GLN B 152 PRO B 153 0 -6.13 CISPEP 5 TYR B 415 PRO B 416 0 -2.21 CISPEP 6 THR B 442 PRO B 443 0 -3.85 CRYST1 79.890 82.840 157.880 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 0.012517 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012071 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006334 0.00000