HEADER SUGAR BINDING PROTEIN 14-SEP-09 3JU9 TITLE CRYSTAL STRUCTURE OF A LECTIN FROM CANAVALIA BRASILIENSIS SEED (CONBR) TITLE 2 COMPLEXED WITH ALPHA-AMINOBUTYRIC ACID COMPND MOL_ID: 1; COMPND 2 MOLECULE: CONCANAVALIN-BR; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: CON BR SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CANAVALIA BRASILIENSIS; SOURCE 3 ORGANISM_COMMON: BRAZILIAN JACK BEAN; SOURCE 4 ORGANISM_TAXID: 61861 KEYWDS CONBR, LECTIN, AGGLUTININ, CANAVALIA BRASILIENSIS, MANGANESE, METAL- KEYWDS 2 BINDING, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.H.S.BEZERRA,B.A.M.ROCHA,C.S.NAGANO,G.A.BEZERRA,T.R.MOURA, AUTHOR 2 M.J.B.BEZERRA,R.G.BENEVIDES,E.S.MARINHO,P.DELATORRE,B.S.CAVADA REVDAT 4 22-NOV-23 3JU9 1 REMARK REVDAT 3 06-SEP-23 3JU9 1 REMARK LINK REVDAT 2 29-JUN-11 3JU9 1 JRNL REVDAT 1 08-DEC-10 3JU9 0 JRNL AUTH E.H.BEZERRA,B.A.ROCHA,C.S.NAGANO,G.A.BEZERRA,T.R.MOURA, JRNL AUTH 2 M.J.BEZERRA,R.G.BENEVIDES,A.H.SAMPAIO,A.M.ASSREUY, JRNL AUTH 3 P.DELATORRE,B.S.CAVADA JRNL TITL STRUCTURAL ANALYSIS OF CONBR REVEALS MOLECULAR CORRELATION JRNL TITL 2 BETWEEN THE CARBOHYDRATE RECOGNITION DOMAIN AND ENDOTHELIAL JRNL TITL 3 NO SYNTHASE ACTIVATION. JRNL REF BIOCHEM.BIOPHYS.RES.COMMUN. V. 408 566 2011 JRNL REFN ISSN 0006-291X JRNL PMID 21530490 JRNL DOI 10.1016/J.BBRC.2011.04.061 REMARK 2 REMARK 2 RESOLUTION. 2.10 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 2.10 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.51 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 14017 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) : 0.207 REMARK 3 R VALUE (WORKING SET) : 0.204 REMARK 3 FREE R VALUE : 0.253 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 749 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) : 2.10 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.16 REMARK 3 REFLECTION IN BIN (WORKING SET) : 940 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 90.41 REMARK 3 BIN R VALUE (WORKING SET) : 0.2450 REMARK 3 BIN FREE R VALUE SET COUNT : 50 REMARK 3 BIN FREE R VALUE : 0.2780 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1807 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 17 REMARK 3 SOLVENT ATOMS : 139 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.54 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.02000 REMARK 3 B22 (A**2) : 0.01000 REMARK 3 B33 (A**2) : -0.02000 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): 0.247 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.203 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.153 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.626 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.945 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.912 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1860 ; 0.015 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2531 ; 1.719 ; 1.944 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 236 ; 9.771 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 77 ;39.252 ;24.545 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 291 ;13.992 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;12.018 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 290 ; 0.243 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1408 ; 0.006 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 803 ; 0.221 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1216 ; 0.303 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 128 ; 0.180 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 5 ; 0.069 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 52 ; 0.200 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 13 ; 0.203 ; 0.200 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): 1214 ; 1.101 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1915 ; 1.569 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 741 ; 2.333 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 616 ; 3.089 ; 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 : 1.20 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 REMARK 4 REMARK 4 3JU9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-SEP-09. REMARK 100 THE DEPOSITION ID IS D_1000055166. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUL-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS REMARK 200 BEAMLINE : D03B-MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.42 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14784 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.775 REMARK 200 RESOLUTION RANGE LOW (A) : 58.930 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.06900 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) : 2.10 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.21 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.19600 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: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1AZD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.8 M AMMONIUM SULFATE, 0.2 M SODIUM REMARK 280 CHLORIDE, 0.1 M HEPES, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293.0K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+1/2 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 34.16150 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 36.51000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.77100 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 34.16150 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 36.51000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.77100 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 34.16150 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 36.51000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 49.77100 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 34.16150 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 36.51000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 49.77100 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: 11990 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -188.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 3 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 350 BIOMT1 4 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 344 LIES ON A SPECIAL POSITION. 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 GLU A 122 ND2 ASN A 131 4555 1.07 REMARK 500 O GLU A 122 CG ASN A 131 4555 2.08 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 118 N - CA - C ANGL. DEV. = 19.9 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 SER A 21 30.35 -92.05 REMARK 500 ALA A 63 116.26 -160.57 REMARK 500 ASN A 104 65.71 -117.37 REMARK 500 SER A 119 52.95 91.85 REMARK 500 HIS A 121 -155.81 -101.44 REMARK 500 THR A 123 127.67 89.89 REMARK 500 PRO A 202 31.65 -95.54 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 A 118 SER A 119 31.57 REMARK 500 SER A 119 THR A 120 -86.39 REMARK 500 HIS A 121 GLU A 122 -111.02 REMARK 500 GLU A 122 THR A 123 95.84 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 MN A 241 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 8 OE2 REMARK 620 2 ASP A 10 OD2 86.2 REMARK 620 3 ASP A 19 OD1 167.8 101.4 REMARK 620 4 HIS A 24 NE2 96.7 85.0 93.4 REMARK 620 5 HOH A 246 O 84.6 89.5 86.0 174.3 REMARK 620 6 HOH A 260 O 91.8 176.2 81.2 92.0 93.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 240 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 10 OD1 REMARK 620 2 ASP A 10 OD2 50.1 REMARK 620 3 TYR A 12 O 73.8 111.9 REMARK 620 4 ASN A 14 OD1 149.5 160.3 83.8 REMARK 620 5 ASP A 19 OD2 104.8 78.5 82.9 92.3 REMARK 620 6 HOH A 244 O 71.0 101.1 91.8 89.7 174.1 REMARK 620 7 HOH A 245 O 108.2 71.7 175.9 93.1 99.7 85.7 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DBB A 238 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 239 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 240 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 241 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 242 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 243 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1AZD RELATED DB: PDB DBREF 3JU9 A 1 237 UNP P55915 CONA_CANBR 1 237 SEQRES 1 A 237 ALA ASP THR ILE VAL ALA VAL GLU LEU ASP THR TYR PRO SEQRES 2 A 237 ASN THR ASP ILE GLY ASP PRO SER TYR PRO HIS ILE GLY SEQRES 3 A 237 ILE ASP ILE LYS SER VAL ARG SER LYS LYS THR ALA LYS SEQRES 4 A 237 TRP ASN MET GLN ASN GLY LYS VAL GLY THR ALA HIS ILE SEQRES 5 A 237 ILE TYR ASN SER VAL GLY LYS ARG LEU SER ALA VAL VAL SEQRES 6 A 237 SER TYR PRO ASN GLY ASP SER ALA THR VAL SER TYR ASP SEQRES 7 A 237 VAL ASP LEU ASP ASN VAL LEU PRO GLU TRP VAL ARG VAL SEQRES 8 A 237 GLY LEU SER ALA SER THR GLY LEU TYR LYS GLU THR ASN SEQRES 9 A 237 THR ILE LEU SER TRP SER PHE THR SER LYS LEU LYS SER SEQRES 10 A 237 ASN SER THR HIS GLU THR ASN ALA LEU HIS PHE MET PHE SEQRES 11 A 237 ASN GLN PHE SER LYS ASP GLN LYS ASP LEU ILE LEU GLN SEQRES 12 A 237 GLY ASP ALA THR THR GLY THR GLU GLY ASN LEU ARG LEU SEQRES 13 A 237 THR ARG VAL SER SER ASN GLY SER PRO GLN GLY SER SER SEQRES 14 A 237 VAL GLY ARG ALA LEU PHE TYR ALA PRO VAL HIS ILE TRP SEQRES 15 A 237 GLU SER SER ALA VAL VAL ALA SER PHE GLU ALA THR PHE SEQRES 16 A 237 THR PHE LEU ILE LYS SER PRO ASP SER HIS PRO ALA ASP SEQRES 17 A 237 GLY ILE ALA PHE PHE ILE SER ASN ILE ASP SER SER ILE SEQRES 18 A 237 PRO SER GLY SER THR GLY ARG LEU LEU GLY LEU PHE PRO SEQRES 19 A 237 ASP ALA ASN HET DBB A 238 7 HET GOL A 239 6 HET CA A 240 1 HET MN A 241 1 HET CL A 242 1 HET CL A 243 1 HETNAM DBB D-ALPHA-AMINOBUTYRIC ACID HETNAM GOL GLYCEROL HETNAM CA CALCIUM ION HETNAM MN MANGANESE (II) ION HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 DBB C4 H9 N O2 FORMUL 3 GOL C3 H8 O3 FORMUL 4 CA CA 2+ FORMUL 5 MN MN 2+ FORMUL 6 CL 2(CL 1-) FORMUL 8 HOH *139(H2 O) HELIX 1 1 ASP A 80 VAL A 84 5 5 HELIX 2 2 THR A 226 LEU A 230 5 5 SHEET 1 A 7 LYS A 36 LYS A 39 0 SHEET 2 A 7 HIS A 24 ILE A 29 -1 N ILE A 25 O ALA A 38 SHEET 3 A 7 ILE A 4 ASP A 10 -1 N ALA A 6 O ASP A 28 SHEET 4 A 7 GLY A 209 SER A 215 -1 O ILE A 210 N LEU A 9 SHEET 5 A 7 TRP A 88 THR A 97 -1 N SER A 94 O ALA A 211 SHEET 6 A 7 SER A 169 PHE A 175 -1 O ALA A 173 N LEU A 93 SHEET 7 A 7 LEU A 140 GLY A 144 -1 N GLN A 143 O ARG A 172 SHEET 1 B 6 LYS A 36 LYS A 39 0 SHEET 2 B 6 HIS A 24 ILE A 29 -1 N ILE A 25 O ALA A 38 SHEET 3 B 6 ILE A 4 ASP A 10 -1 N ALA A 6 O ASP A 28 SHEET 4 B 6 GLY A 209 SER A 215 -1 O ILE A 210 N LEU A 9 SHEET 5 B 6 TRP A 88 THR A 97 -1 N SER A 94 O ALA A 211 SHEET 6 B 6 VAL A 179 HIS A 180 -1 O VAL A 179 N VAL A 89 SHEET 1 C 6 SER A 72 ASP A 78 0 SHEET 2 C 6 ARG A 60 SER A 66 -1 N LEU A 61 O TYR A 77 SHEET 3 C 6 VAL A 47 ASN A 55 -1 N ILE A 53 O SER A 62 SHEET 4 C 6 VAL A 188 LEU A 198 -1 O ALA A 193 N ILE A 52 SHEET 5 C 6 THR A 105 LYS A 116 -1 N LYS A 116 O VAL A 188 SHEET 6 C 6 ASN A 124 PHE A 130 -1 O ASN A 124 N LEU A 115 SHEET 1 D 7 SER A 72 ASP A 78 0 SHEET 2 D 7 ARG A 60 SER A 66 -1 N LEU A 61 O TYR A 77 SHEET 3 D 7 VAL A 47 ASN A 55 -1 N ILE A 53 O SER A 62 SHEET 4 D 7 VAL A 188 LEU A 198 -1 O ALA A 193 N ILE A 52 SHEET 5 D 7 THR A 105 LYS A 116 -1 N LYS A 116 O VAL A 188 SHEET 6 D 7 LEU A 154 ARG A 155 -1 O LEU A 154 N ILE A 106 SHEET 7 D 7 THR A 147 THR A 148 -1 N THR A 147 O ARG A 155 LINK OE2 GLU A 8 MN MN A 241 1555 1555 2.28 LINK OD1 ASP A 10 CA CA A 240 1555 1555 2.50 LINK OD2 ASP A 10 CA CA A 240 1555 1555 2.71 LINK OD2 ASP A 10 MN MN A 241 1555 1555 2.14 LINK O TYR A 12 CA CA A 240 1555 1555 2.34 LINK OD1 ASN A 14 CA CA A 240 1555 1555 2.40 LINK OD2 ASP A 19 CA CA A 240 1555 1555 2.36 LINK OD1 ASP A 19 MN MN A 241 1555 1555 2.45 LINK NE2 HIS A 24 MN MN A 241 1555 1555 2.17 LINK CA CA A 240 O HOH A 244 1555 1555 2.34 LINK CA CA A 240 O HOH A 245 1555 1555 2.34 LINK MN MN A 241 O HOH A 246 1555 1555 2.07 LINK MN MN A 241 O HOH A 260 1555 1555 2.37 CISPEP 1 ALA A 207 ASP A 208 0 1.11 SITE 1 AC1 10 SER A 113 ASN A 124 ALA A 125 MET A 129 SITE 2 AC1 10 PHE A 130 ASP A 139 VAL A 179 HIS A 180 SITE 3 AC1 10 HOH A 254 HOH A 271 SITE 1 AC2 8 TYR A 12 ASN A 14 GLY A 98 LEU A 99 SITE 2 AC2 8 TYR A 100 ALA A 207 ASP A 208 ARG A 228 SITE 1 AC3 6 ASP A 10 TYR A 12 ASN A 14 ASP A 19 SITE 2 AC3 6 HOH A 244 HOH A 245 SITE 1 AC4 6 GLU A 8 ASP A 10 ASP A 19 HIS A 24 SITE 2 AC4 6 HOH A 246 HOH A 260 SITE 1 AC5 1 ALA A 236 SITE 1 AC6 3 ASN A 14 ARG A 228 HOH A 382 CRYST1 68.323 73.020 99.542 90.00 90.00 90.00 I 2 2 2 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 0.014636 0.000000 0.000000 0.00000 SCALE2 0.000000 0.013695 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010046 0.00000