HEADER HYDROLASE 17-JAN-12 4DCF TITLE STRUCTURE OF MTX-II FROM BOTHROPS BRAZILI CAVEAT 4DCF ATOMIC CLASHES AROUND POTENTIAL DISULFIDE LINKAGES. CAVEAT 2 4DCF INAPPROPRIATE BOND DISTANCE AND ANGLES AT SOME RESIDUES COMPND MOL_ID: 1; COMPND 2 MOLECULE: MTX-II CHAIN A; COMPND 3 CHAIN: A, B, C, D SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOTHROPS BRAZILI; SOURCE 3 ORGANISM_TAXID: 157546 KEYWDS LYS49 PHOSPHOLIPASE, PHOSPHOLIPASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.ULLAH,T.A.C.B.SOUZA,C.BETZEL,M.T.MURAKAMI,R.K.ARNI REVDAT 3 13-SEP-23 4DCF 1 REMARK REVDAT 2 11-SEP-13 4DCF 1 JRNL REVDAT 1 13-JUN-12 4DCF 0 JRNL AUTH A.ULLAH,T.A.SOUZA,C.BETZEL,M.T.MURAKAMI,R.K.ARNI JRNL TITL CRYSTALLOGRAPHIC PORTRAYAL OF DIFFERENT CONFORMATIONAL JRNL TITL 2 STATES OF A LYS49 PHOSPHOLIPASE A2 HOMOLOGUE: INSIGHTS INTO JRNL TITL 3 STRUCTURAL DETERMINANTS FOR MYOTOXICITY AND DIMERIC JRNL TITL 4 CONFIGURATION. JRNL REF INT.J.BIOL.MACROMOL. V. 51 209 2012 JRNL REFN ISSN 0141-8130 JRNL PMID 22584077 JRNL DOI 10.1016/J.IJBIOMAC.2012.05.006 REMARK 2 REMARK 2 RESOLUTION. 2.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 2.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.72 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.9 REMARK 3 NUMBER OF REFLECTIONS : 11881 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) : 0.228 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.320 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 629 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) : 2.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.77 REMARK 3 REFLECTION IN BIN (WORKING SET) : 757 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 82.84 REMARK 3 BIN R VALUE (WORKING SET) : 0.3060 REMARK 3 BIN FREE R VALUE SET COUNT : 30 REMARK 3 BIN FREE R VALUE : 0.3910 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3837 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 102 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.95 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.10000 REMARK 3 B22 (A**2) : 0.04000 REMARK 3 B33 (A**2) : -0.23000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.16000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.519 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.448 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 22.661 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.915 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.808 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3965 ; 0.012 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5323 ; 1.472 ; 1.990 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 486 ; 6.926 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 163 ;40.077 ;24.601 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 768 ;21.176 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;21.345 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 549 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2892 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2434 ; 0.531 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3902 ; 1.063 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1531 ; 1.396 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1421 ; 2.412 ; 4.500 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 : 1.40 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 REMARK 4 REMARK 4 4DCF COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 20-JAN-12. REMARK 100 THE DEPOSITION ID IS D_1000070154. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.2 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS REMARK 200 BEAMLINE : W01B-MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.458 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12516 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.700 REMARK 200 RESOLUTION RANGE LOW (A) : 20.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.11600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.80 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.33900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.680 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 2H8I REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.72 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS PH 8.2, 25% PEG 4000, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 29.70000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 64.44300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 29.70000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 64.44300 REMARK 290 SMTRY3 4 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 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 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 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 ASN C 109 CG OD1 ND2 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 SG CYS C 49 SG CYS C 122 0.63 REMARK 500 SG CYS A 57 SG CYS A 81 0.87 REMARK 500 SG CYS B 57 SG CYS B 81 1.79 REMARK 500 SG CYS C 50 SG CYS C 88 1.80 REMARK 500 CB CYS C 49 SG CYS C 122 1.94 REMARK 500 O ASN D 110 N LEU D 112 2.01 REMARK 500 OH TYR C 24 OD2 ASP C 38 2.02 REMARK 500 CB ASP A 58 OD1 ASP A 62 2.03 REMARK 500 O LEU D 112 N PRO D 114 2.08 REMARK 500 O CYS C 81 N LYS C 83 2.15 REMARK 500 OH TYR A 24 OD2 ASP A 38 2.19 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 OD1 ASN A 110 NZ LYS D 19 1556 1.57 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS C 122 C CYS C 122 OXT 0.390 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 109 CB - CA - C ANGL. DEV. = -33.6 DEGREES REMARK 500 ASN A 110 N - CA - CB ANGL. DEV. = 32.9 DEGREES REMARK 500 ASN A 110 N - CA - C ANGL. DEV. = -16.6 DEGREES REMARK 500 PRO A 114 C - N - CD ANGL. DEV. = -18.4 DEGREES REMARK 500 ASN B 27 CB - CA - C ANGL. DEV. = 39.5 DEGREES REMARK 500 ASN B 27 N - CA - C ANGL. DEV. = -28.2 DEGREES REMARK 500 ASN B 109 CB - CA - C ANGL. DEV. = 35.2 DEGREES REMARK 500 ASN B 110 N - CA - C ANGL. DEV. = -39.2 DEGREES REMARK 500 PRO C 121 C - N - CD ANGL. DEV. = -31.5 DEGREES REMARK 500 THR D 13 CB - CA - C ANGL. DEV. = 29.9 DEGREES REMARK 500 GLY D 14 N - CA - C ANGL. DEV. = -21.7 DEGREES REMARK 500 CYS D 88 CA - CB - SG ANGL. DEV. = 7.7 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 ASP A 56 2.29 111.18 REMARK 500 LYS A 61 7.77 -152.37 REMARK 500 GLU A 77 -81.81 -59.22 REMARK 500 ASN A 78 -167.93 60.05 REMARK 500 ASN A 109 109.10 -42.00 REMARK 500 ASN A 110 -37.41 151.23 REMARK 500 LEU A 112 103.59 26.33 REMARK 500 LYS A 113 -174.17 -43.60 REMARK 500 ASN B 27 -140.99 -132.66 REMARK 500 CYS B 28 73.56 60.93 REMARK 500 VAL B 30 169.07 -43.97 REMARK 500 ASP B 56 -49.16 -167.78 REMARK 500 GLU B 77 70.39 -100.09 REMARK 500 ASN B 78 -149.90 -80.35 REMARK 500 ASN B 109 -115.69 109.11 REMARK 500 ASN B 110 -38.19 -139.72 REMARK 500 HIS B 111 39.11 137.51 REMARK 500 LYS B 113 113.67 -19.80 REMARK 500 LEU C 2 -72.25 -22.01 REMARK 500 VAL C 30 -119.89 -115.82 REMARK 500 ASN C 78 -168.54 -23.95 REMARK 500 SER C 80 -61.27 29.19 REMARK 500 LEU C 82 -40.53 -20.56 REMARK 500 TYR C 107 77.61 -100.67 REMARK 500 ASN C 110 98.64 63.44 REMARK 500 HIS C 111 7.98 110.08 REMARK 500 LEU C 112 95.95 141.34 REMARK 500 PRO C 121 130.04 15.75 REMARK 500 GLU D 12 -114.39 -83.20 REMARK 500 THR D 13 -99.58 3.08 REMARK 500 LYS D 19 34.65 -78.65 REMARK 500 SER D 20 -59.11 -165.07 REMARK 500 ALA D 23 28.99 -153.87 REMARK 500 ASN D 27 -47.11 -147.27 REMARK 500 CYS D 28 107.69 -43.64 REMARK 500 ASP D 38 -142.50 -105.69 REMARK 500 LYS D 53 38.23 -84.13 REMARK 500 ASP D 56 -88.35 84.17 REMARK 500 CYS D 57 144.87 -31.66 REMARK 500 ASP D 58 75.04 -110.56 REMARK 500 LYS D 71 -31.98 74.85 REMARK 500 GLU D 77 36.98 -81.20 REMARK 500 ASN D 78 -155.68 -57.86 REMARK 500 LEU D 100 4.42 -63.35 REMARK 500 TYR D 107 64.30 -118.65 REMARK 500 ARG D 108 148.02 176.84 REMARK 500 ASN D 110 -66.93 -165.75 REMARK 500 HIS D 111 -52.20 41.98 REMARK 500 LYS D 113 -49.36 -12.63 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN C 79 SER C 80 144.60 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 PG4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PG4 B 201 DBREF 4DCF A 1 122 PDB 4DCF 4DCF 1 122 DBREF 4DCF B 1 122 PDB 4DCF 4DCF 1 122 DBREF 4DCF C 1 122 PDB 4DCF 4DCF 1 122 DBREF 4DCF D 1 122 PDB 4DCF 4DCF 1 122 SEQRES 1 A 122 SER LEU VAL GLU LEU GLY LYS MET ILE LEU GLN GLU THR SEQRES 2 A 122 GLY LYS ASN PRO ALA LYS SER TYR GLY ALA TYR GLY CYS SEQRES 3 A 122 ASN CYS GLY VAL LEU GLY ARG GLY LYS PRO LYS ASP ALA SEQRES 4 A 122 THR ASP ARG CYS CYS TYR VAL HIS LYS CYS CYS TYR LYS SEQRES 5 A 122 LYS LEU THR ASP CYS ASP PRO LYS LYS ASP ARG TYR SER SEQRES 6 A 122 TYR SER TRP LYS ASP LYS THR ILE VAL CYS GLY GLU ASN SEQRES 7 A 122 ASN SER CYS LEU LYS GLU LEU CYS GLU CYS ASP LYS ALA SEQRES 8 A 122 VAL ALA ILE CYS LEU ARG GLU ASN LEU ASP THR TYR ASN SEQRES 9 A 122 LYS LYS TYR ARG ASN ASN HIS LEU LYS PRO PHE CYS LYS SEQRES 10 A 122 LYS ALA ASP PRO CYS SEQRES 1 B 122 SER LEU VAL GLU LEU GLY LYS MET ILE LEU GLN GLU THR SEQRES 2 B 122 GLY LYS ASN PRO ALA LYS SER TYR GLY ALA TYR GLY CYS SEQRES 3 B 122 ASN CYS GLY VAL LEU GLY ARG GLY LYS PRO LYS ASP ALA SEQRES 4 B 122 THR ASP ARG CYS CYS TYR VAL HIS LYS CYS CYS TYR LYS SEQRES 5 B 122 LYS LEU THR ASP CYS ASP PRO LYS LYS ASP ARG TYR SER SEQRES 6 B 122 TYR SER TRP LYS ASP LYS THR ILE VAL CYS GLY GLU ASN SEQRES 7 B 122 ASN SER CYS LEU LYS GLU LEU CYS GLU CYS ASP LYS ALA SEQRES 8 B 122 VAL ALA ILE CYS LEU ARG GLU ASN LEU ASP THR TYR ASN SEQRES 9 B 122 LYS LYS TYR ARG ASN ASN HIS LEU LYS PRO PHE CYS LYS SEQRES 10 B 122 LYS ALA ASP PRO CYS SEQRES 1 C 122 SER LEU VAL GLU LEU GLY LYS MET ILE LEU GLN GLU THR SEQRES 2 C 122 GLY LYS ASN PRO ALA LYS SER TYR GLY ALA TYR GLY CYS SEQRES 3 C 122 ASN CYS GLY VAL LEU GLY ARG GLY LYS PRO LYS ASP ALA SEQRES 4 C 122 THR ASP ARG CYS CYS TYR VAL HIS LYS CYS CYS TYR LYS SEQRES 5 C 122 LYS LEU THR ASP CYS ASP PRO LYS LYS ASP ARG TYR SER SEQRES 6 C 122 TYR SER TRP LYS ASP LYS THR ILE VAL CYS GLY GLU ASN SEQRES 7 C 122 ASN SER CYS LEU LYS GLU LEU CYS GLU CYS ASP LYS ALA SEQRES 8 C 122 VAL ALA ILE CYS LEU ARG GLU ASN LEU ASP THR TYR ASN SEQRES 9 C 122 LYS LYS TYR ARG ASN ASN HIS LEU LYS PRO PHE CYS LYS SEQRES 10 C 122 LYS ALA ASP PRO CYS SEQRES 1 D 122 SER LEU VAL GLU LEU GLY LYS MET ILE LEU GLN GLU THR SEQRES 2 D 122 GLY LYS ASN PRO ALA LYS SER TYR GLY ALA TYR GLY CYS SEQRES 3 D 122 ASN CYS GLY VAL LEU GLY ARG GLY LYS PRO LYS ASP ALA SEQRES 4 D 122 THR ASP ARG CYS CYS TYR VAL HIS LYS CYS CYS TYR LYS SEQRES 5 D 122 LYS LEU THR ASP CYS ASP PRO LYS LYS ASP ARG TYR SER SEQRES 6 D 122 TYR SER TRP LYS ASP LYS THR ILE VAL CYS GLY GLU ASN SEQRES 7 D 122 ASN SER CYS LEU LYS GLU LEU CYS GLU CYS ASP LYS ALA SEQRES 8 D 122 VAL ALA ILE CYS LEU ARG GLU ASN LEU ASP THR TYR ASN SEQRES 9 D 122 LYS LYS TYR ARG ASN ASN HIS LEU LYS PRO PHE CYS LYS SEQRES 10 D 122 LYS ALA ASP PRO CYS HET PG4 A 201 13 HET PG4 B 201 13 HETNAM PG4 TETRAETHYLENE GLYCOL FORMUL 5 PG4 2(C8 H18 O5) FORMUL 7 HOH *102(H2 O) HELIX 1 1 SER A 1 GLY A 14 1 14 HELIX 2 2 ASN A 16 GLY A 22 1 7 HELIX 3 3 ASP A 38 LYS A 53 1 16 HELIX 4 4 ASN A 79 ASN A 99 1 21 HELIX 5 5 ASN A 104 ARG A 108 5 5 HELIX 6 6 LEU B 2 GLY B 14 1 13 HELIX 7 7 ASN B 16 GLY B 22 1 7 HELIX 8 8 ASP B 38 LEU B 54 1 17 HELIX 9 9 ASN B 79 ASN B 99 1 21 HELIX 10 10 ASN B 104 ASN B 109 5 6 HELIX 11 11 LEU C 2 THR C 13 1 12 HELIX 12 12 ASN C 16 GLY C 22 1 7 HELIX 13 13 ASP C 38 LYS C 53 1 16 HELIX 14 14 CYS C 81 ASN C 99 1 19 HELIX 15 15 LEU D 2 GLU D 12 1 11 HELIX 16 16 PRO D 17 GLY D 22 1 6 HELIX 17 17 ALA D 39 LYS D 53 1 15 HELIX 18 18 ASN D 79 ASN D 99 1 21 HELIX 19 19 LEU D 112 CYS D 116 5 5 SHEET 1 A 2 TYR A 66 LYS A 69 0 SHEET 2 A 2 THR A 72 CYS A 75 -1 O THR A 72 N LYS A 69 SHEET 1 B 2 TYR B 66 TRP B 68 0 SHEET 2 B 2 ILE B 73 CYS B 75 -1 O VAL B 74 N SER B 67 SHEET 1 C 2 TYR C 66 LYS C 69 0 SHEET 2 C 2 THR C 72 CYS C 75 -1 O VAL C 74 N SER C 67 SHEET 1 D 2 TYR D 66 LYS D 69 0 SHEET 2 D 2 THR D 72 CYS D 75 -1 O VAL D 74 N SER D 67 SSBOND 1 CYS A 26 CYS A 116 1555 1555 2.04 SSBOND 2 CYS A 28 CYS A 44 1555 1555 2.07 SSBOND 3 CYS A 43 CYS A 95 1555 1555 2.08 SSBOND 4 CYS A 49 CYS A 122 1555 1555 2.07 SSBOND 5 CYS A 50 CYS A 88 1555 1555 2.06 SSBOND 6 CYS A 75 CYS A 86 1555 1555 2.06 SSBOND 7 CYS B 26 CYS B 116 1555 1555 2.05 SSBOND 8 CYS B 28 CYS B 44 1555 1555 2.09 SSBOND 9 CYS B 43 CYS B 95 1555 1555 2.08 SSBOND 10 CYS B 49 CYS B 122 1555 1555 2.07 SSBOND 11 CYS B 50 CYS B 88 1555 1555 2.05 SSBOND 12 CYS B 75 CYS B 86 1555 1555 2.06 SSBOND 13 CYS C 26 CYS C 116 1555 1555 2.05 SSBOND 14 CYS C 28 CYS C 44 1555 1555 2.07 SSBOND 15 CYS C 43 CYS C 95 1555 1555 2.04 SSBOND 16 CYS C 57 CYS C 81 1555 1555 1.99 SSBOND 17 CYS C 75 CYS C 86 1555 1555 2.06 SSBOND 18 CYS D 26 CYS D 116 1555 1555 2.05 SSBOND 19 CYS D 28 CYS D 44 1555 1555 2.51 SSBOND 20 CYS D 43 CYS D 95 1555 1555 2.05 SSBOND 21 CYS D 49 CYS D 122 1555 1555 2.08 SSBOND 22 CYS D 50 CYS D 88 1555 1555 2.26 SSBOND 23 CYS D 57 CYS D 81 1555 1555 1.90 SSBOND 24 CYS D 75 CYS D 86 1555 1555 2.04 CISPEP 1 ARG D 108 ASN D 109 0 8.78 SITE 1 AC1 7 LEU A 2 PRO A 17 TYR A 21 ASN A 27 SITE 2 AC1 7 GLY A 29 LYS A 48 HOH A 320 SITE 1 AC2 5 LEU B 2 GLY B 6 PRO B 17 TYR B 21 SITE 2 AC2 5 GLY B 29 CRYST1 59.400 128.886 67.008 90.00 105.66 90.00 C 1 2 1 16 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.016835 0.000000 0.004719 0.00000 SCALE2 0.000000 0.007759 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015499 0.00000