10 20 30 40 50 60 70 80 2CYF - Header ----|----|----|----|----|----|----|----|----|----|----|----|----|----|----|----| Asymmetric UnitHEADER METAL BINDING PROTEIN 06-JUL-05 2CYF
TITLE THE CRYSTAL STRUCTURE OF CANAVALIA MARITIMA LECTIN (CONM) TITLE 2 IN COMPLEX WITH TREHALOSE AND MALTOSE
COMPND MOL_ID: 1; COMPND 2 MOLECULE: LECTIN; COMPND 3 CHAIN: A, C
SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: CANAVALIA MARITIMA; SOURCE 3 ORGANISM_TAXID: 3825; SOURCE 4 TISSUE: SEEDS
KEYWDS CANACALIA MARITIMA, LECTIN, MALTOSE, CRYSTAL STRUCTURE, KEYWDS 2 METAL BINDING PROTEIN
EXPDTA X-RAY DIFFRACTION
AUTHOR P.DELATORRE,B.A.M.ROCHA,E.P.SOUSA,C.A.A.GADELHA,W.F.AZEVEDO AUTHOR 2 JR.,B.S.CAVADA
REVDAT 2 24-FEB-09 2CYF 1 VERSN REVDAT 1 13-JUN-06 2CYF 0
JRNL AUTH P.DELATORRE,B.A.M.ROCHA,C.A.A.GADELHA, JRNL AUTH 2 T.SANTI-GADELHA,J.B.CAJAZEIRAS,E.P.SOUZA, JRNL AUTH 3 K.S.NASCIMENTO,V.N.FREIRE,A.H.SAMPAIO, JRNL AUTH 4 W.F.AZEVEDO JR.,B.S.CAVADA JRNL TITL CRYSTAL STRUCTURE OF A LECTIN FROM CANAVALIA JRNL TITL 2 MARITIMA (CONM) IN COMPLEX WITH TREHALOSE AND JRNL TITL 3 MALTOSE REVEALS RELEVANT MUTATION IN CONA-LIKE JRNL TITL 4 LECTINS JRNL REF J.STRUCT.BIOL. V. 154 280 2006 JRNL REFN ISSN 1047-8477 JRNL PMID 16677825 JRNL DOI 10.1016/J.JSB.2006.03.011
REMARK 1
REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS.
REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0003 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 9.98 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.800 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 39189 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) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4362 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.84 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2776 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.61 REMARK 3 BIN R VALUE (WORKING SET) : 0.2210 REMARK 3 BIN FREE R VALUE SET COUNT : 307 REMARK 3 BIN FREE R VALUE : 0.2860 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3502 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 327 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.03000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : -0.03000 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): 0.146 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.140 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.086 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.691 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.949 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.926 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3625 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 3181 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4940 ; 1.869 ; 1.942 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7432 ; 0.905 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 456 ; 7.966 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 148 ;33.677 ;24.730 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 556 ;14.729 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;15.463 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 580 ; 0.113 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4014 ; 0.007 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 710 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 917 ; 0.253 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 3847 ; 0.220 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1898 ; 0.198 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2408 ; 0.103 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 390 ; 0.217 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): 1 ; 0.080 ; 0.200 REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 11 ; 0.078 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 28 ; 0.306 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 89 ; 0.215 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 24 ; 0.364 ; 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): 2302 ; 1.008 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 942 ; 0.286 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3697 ; 1.633 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1465 ; 2.456 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1243 ; 3.644 ; 4.500 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 REMARK 3 RIDING POSITIONS
REMARK 4 REMARK 4 2CYF COMPLIES WITH FORMAT V. 3.15, 01-DEC-08
REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 11-JUL-05. REMARK 100 THE RCSB ID CODE IS RCSB024768.
REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-AUG-04 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 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) : 1.43 REMARK 200 MONOCHROMATOR : SAGITALLY FOCUSED SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MAR REMARK 200 DATA SCALING SOFTWARE : CCP4 (SCALA) REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50831 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 9.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.91 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.9 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 <I/SIGMA(I)> 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: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL
REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.30 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: HEPES-NA, AMMONIUM SULFATE, PEG REMARK 280 400, PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K
REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+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 33.51650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 48.66600 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 33.51650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 48.66600 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 300 REMARK: THE BIOLOGICAL ASSEMBLY IS A TETRAMER GENERATED FROM THE REMARK 300 DIMER IN THE ASYMMETRIC UNIT
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 APPLY THE FOLLOWING TO CHAINS: A, C REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 67.03300 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 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 SER A 117 REMARK 465 ASN A 118 REMARK 465 SER A 119 REMARK 465 THR A 120 REMARK 465 HIS A 121 REMARK 465 GLU A 122 REMARK 465 LEU A 198 REMARK 465 SER C 117 REMARK 465 ASN C 118 REMARK 465 SER C 119 REMARK 465 THR C 120 REMARK 465 HIS C 121 REMARK 465 GLU C 122
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 O HOH A 316 O HOH A 477 1.49 REMARK 500 O HOH A 249 O HOH A 533 1.55 REMARK 500 NE ARG C 172 O HOH C 474 1.67 REMARK 500 CB SER A 72 O HOH A 505 1.72 REMARK 500 CB SER C 113 O HOH C 487 1.75 REMARK 500 CB SER A 113 O HOH A 497 1.77 REMARK 500 NE ARG A 172 O HOH A 515 1.80 REMARK 500 O HOH A 539 O HOH A 567 1.83 REMARK 500 OG SER A 72 O HOH A 505 1.91 REMARK 500 ND2 ASN A 69 O HOH A 539 1.93 REMARK 500 OG SER A 113 O HOH A 497 1.93 REMARK 500 OE2 GLU C 87 O HOH C 546 1.96 REMARK 500 CB VAL A 170 O HOH A 558 2.06 REMARK 500 CG ARG A 172 O HOH A 515 2.06 REMARK 500 OE1 GLN C 143 CD ARG C 172 2.06 REMARK 500 CB ASP C 192 O HOH C 531 2.15 REMARK 500 O HOH C 380 O HOH C 444 2.15 REMARK 500 O HOH C 285 O HOH C 457 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 VAL A 64 CB - CA - C ANGL. DEV. = -15.4 DEGREES REMARK 500 ARG A 172 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 172 NE - CZ - NH2 ANGL. DEV. = -6.9 DEGREES REMARK 500 ASP C 16 CB - CG - OD2 ANGL. DEV. = 5.5 DEGREES REMARK 500 LYS C 30 CD - CE - NZ ANGL. DEV. = 14.1 DEGREES REMARK 500 VAL C 64 CB - CA - C ANGL. DEV. = -15.1 DEGREES REMARK 500 ASP C 71 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG C 172 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG C 172 NE - CZ - NH2 ANGL. DEV. = -5.4 DEGREES REMARK 500 ASP C 192 CB - CG - OD2 ANGL. DEV. = 7.5 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 SER A 21 48.49 -90.89 REMARK 500 THR A 226 -179.07 -65.93 REMARK 500 ASN C 14 76.05 -101.78 REMARK 500 SER C 21 42.60 -86.82 REMARK 500 LYS C 30 17.26 57.66 REMARK 500 ASP C 136 79.81 -114.21 REMARK 500 SER C 168 47.32 39.55 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 THR A 148 GLY A 149 148.64 REMARK 500 REMARK 500 REMARK: NULL
REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 346 DISTANCE = 5.30 ANGSTROMS REMARK 525 HOH A 362 DISTANCE = 5.89 ANGSTROMS REMARK 525 HOH A 408 DISTANCE = 6.33 ANGSTROMS REMARK 525 HOH C 400 DISTANCE = 5.67 ANGSTROMS REMARK 525 HOH A 449 DISTANCE = 5.26 ANGSTROMS REMARK 525 HOH C 437 DISTANCE = 6.25 ANGSTROMS REMARK 525 HOH C 458 DISTANCE = 5.05 ANGSTROMS REMARK 525 HOH A 565 DISTANCE = 6.34 ANGSTROMS
REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 MAL A 240 REMARK 610 MAL C 1240
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 CA A 238 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 10 OD2 REMARK 620 2 TYR A 12 O 112.3 REMARK 620 3 ASN A 14 OD1 156.7 83.9 REMARK 620 4 ASP A 19 OD2 77.8 81.3 88.9 REMARK 620 5 HOH A 562 O 75.6 169.5 86.6 94.2 REMARK 620 6 ASP A 10 OD1 54.0 77.3 149.1 111.8 113.2 REMARK 620 7 HOH A 479 O 113.1 91.0 81.8 168.6 91.9 74.3 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN A 239 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 8 OE1 REMARK 620 2 ASP A 10 OD2 95.7 REMARK 620 3 ASP A 19 OD1 171.7 91.6 REMARK 620 4 HIS A 24 NE2 91.6 87.2 92.6 REMARK 620 5 HOH A 483 O 86.8 93.6 88.9 178.3 REMARK 620 6 HOH A 551 O 86.2 174.6 86.8 87.8 91.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA C 238 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP C 10 OD1 REMARK 620 2 TYR C 12 O 77.0 REMARK 620 3 ASN C 14 OD1 146.5 79.3 REMARK 620 4 ASP C 19 OD2 109.6 79.7 88.9 REMARK 620 5 HOH C 520 O 113.3 169.7 91.5 95.6 REMARK 620 6 ASP C 10 OD2 53.3 114.0 160.2 79.8 73.7 REMARK 620 7 HOH C 500 O 72.3 91.1 84.8 169.7 92.8 108.5 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MN C 239 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU C 8 OE1 REMARK 620 2 ASP C 10 OD2 94.7 REMARK 620 3 ASP C 19 OD1 170.3 94.3 REMARK 620 4 HIS C 24 NE2 94.2 85.7 90.1 REMARK 620 5 HOH C 524 O 85.6 90.2 90.7 175.9 REMARK 620 6 HOH C 566 O 87.2 175.4 84.1 89.9 94.2 REMARK 620 N 1 2 3 4 5
REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAL A 240 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MAL C 1240 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 238 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA C 238 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN C 239 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 239
REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2CWM RELATED DB: PDB REMARK 900 NATIVE CRYSTAL STRUCTURE OF CONM REMARK 900 RELATED ID: 2CY6 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF CONM IN COMPLEX WITH TREHALOSE
DBREF 2CYF A 1 237 PDB 2CYF 2CYF 1 237 DBREF 2CYF C 1 237 PDB 2CYF 2CYF 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 VAL 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 ASP GLY ASN LEU GLU 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 ASP ALA THR PHE SEQRES 16 A 237 THR PHE LEU ILE LYS SER SER 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 SEQRES 1 C 237 ALA ASP THR ILE VAL ALA VAL GLU LEU ASP THR TYR PRO SEQRES 2 C 237 ASN THR ASP ILE GLY ASP PRO SER TYR PRO HIS ILE GLY SEQRES 3 C 237 ILE ASP ILE LYS SER VAL ARG SER LYS LYS THR ALA LYS SEQRES 4 C 237 TRP ASN MET GLN ASN GLY LYS VAL GLY THR ALA HIS ILE SEQRES 5 C 237 ILE TYR ASN SER VAL GLY LYS ARG LEU SER ALA VAL VAL SEQRES 6 C 237 SER TYR PRO ASN GLY ASP SER ALA THR VAL SER TYR ASP SEQRES 7 C 237 VAL ASP LEU ASP ASN VAL LEU PRO GLU TRP VAL ARG VAL SEQRES 8 C 237 GLY LEU SER ALA SER THR GLY LEU TYR LYS GLU THR ASN SEQRES 9 C 237 THR ILE LEU SER TRP SER PHE THR SER LYS LEU LYS SER SEQRES 10 C 237 ASN SER THR HIS GLU THR ASN ALA LEU HIS PHE VAL PHE SEQRES 11 C 237 ASN GLN PHE SER LYS ASP GLN LYS ASP LEU ILE LEU GLN SEQRES 12 C 237 GLY ASP ALA THR THR GLY THR ASP GLY ASN LEU GLU LEU SEQRES 13 C 237 THR ARG VAL SER SER ASN GLY SER PRO GLN GLY SER SER SEQRES 14 C 237 VAL GLY ARG ALA LEU PHE TYR ALA PRO VAL HIS ILE TRP SEQRES 15 C 237 GLU SER SER ALA VAL VAL ALA SER PHE ASP ALA THR PHE SEQRES 16 C 237 THR PHE LEU ILE LYS SER SER ASP SER HIS PRO ALA ASP SEQRES 17 C 237 GLY ILE ALA PHE PHE ILE SER ASN ILE ASP SER SER ILE SEQRES 18 C 237 PRO SER GLY SER THR GLY ARG LEU LEU GLY LEU PHE PRO SEQRES 19 C 237 ASP ALA ASN
HET MAL A 240 22 HET MAL C1240 22 HET CA A 238 1 HET CA C 238 1 HET MN C 239 1 HET MN A 239 1
HETNAM MAL MALTOSE HETNAM CA CALCIUM ION HETNAM MN MANGANESE (II) ION
FORMUL 3 MAL 2(C12 H22 O11) FORMUL 5 CA 2(CA 2+) FORMUL 7 MN 2(MN 2+) FORMUL 9 HOH *327(H2 O)
HELIX 1 1 ASN A 14 GLY A 18 5 5 HELIX 2 2 ASP A 80 VAL A 84 5 5 HELIX 3 3 THR A 226 LEU A 230 5 5 HELIX 4 4 ASN C 14 GLY C 18 5 5 HELIX 5 5 ASP C 80 VAL C 84 5 5 HELIX 6 6 THR C 226 LEU C 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 ASN A 216 -1 O ILE A 210 N LEU A 9 SHEET 5 A 7 TRP A 88 SER A 96 -1 N SER A 94 O ALA A 211 SHEET 6 A 7 VAL A 170 PHE A 175 -1 O PHE A 175 N VAL A 91 SHEET 7 A 7 LEU A 140 GLY A 144 -1 N ILE A 141 O LEU A 174 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 ASN A 216 -1 O ILE A 210 N LEU A 9 SHEET 5 B 6 TRP A 88 SER A 96 -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 C12 SER A 72 ASP A 78 0 SHEET 2 C12 ARG A 60 SER A 66 -1 N LEU A 61 O TYR A 77 SHEET 3 C12 GLY A 48 ASN A 55 -1 N THR A 49 O SER A 66 SHEET 4 C12 VAL A 188 PHE A 197 -1 O PHE A 195 N ALA A 50 SHEET 5 C12 SER A 108 LYS A 116 -1 N SER A 110 O THR A 194 SHEET 6 C12 ASN A 124 PHE A 130 -1 O ASN A 124 N LEU A 115 SHEET 7 C12 ASN C 124 PHE C 130 -1 O HIS C 127 N HIS A 127 SHEET 8 C12 THR C 105 LYS C 116 -1 N TRP C 109 O PHE C 130 SHEET 9 C12 VAL C 188 LEU C 198 -1 O VAL C 188 N LYS C 116 SHEET 10 C12 VAL C 47 ASN C 55 -1 N ILE C 52 O ALA C 193 SHEET 11 C12 ARG C 60 SER C 66 -1 O SER C 62 N ILE C 53 SHEET 12 C12 SER C 72 ASP C 78 -1 O TYR C 77 N LEU C 61 SHEET 1 D10 SER A 72 ASP A 78 0 SHEET 2 D10 ARG A 60 SER A 66 -1 N LEU A 61 O TYR A 77 SHEET 3 D10 GLY A 48 ASN A 55 -1 N THR A 49 O SER A 66 SHEET 4 D10 VAL A 188 PHE A 197 -1 O PHE A 195 N ALA A 50 SHEET 5 D10 SER A 108 LYS A 116 -1 N SER A 110 O THR A 194 SHEET 6 D10 ASN A 124 PHE A 130 -1 O ASN A 124 N LEU A 115 SHEET 7 D10 ASN C 124 PHE C 130 -1 O HIS C 127 N HIS A 127 SHEET 8 D10 THR C 105 LYS C 116 -1 N TRP C 109 O PHE C 130 SHEET 9 D10 LEU C 154 GLU C 155 -1 O LEU C 154 N ILE C 106 SHEET 10 D10 THR C 147 THR C 148 -1 N THR C 147 O GLU C 155 SHEET 1 E 3 THR A 105 ILE A 106 0 SHEET 2 E 3 LEU A 154 GLU A 155 -1 O LEU A 154 N ILE A 106 SHEET 3 E 3 THR A 147 THR A 148 -1 N THR A 147 O GLU A 155 SHEET 1 F 7 LYS C 36 LYS C 39 0 SHEET 2 F 7 HIS C 24 ILE C 29 -1 N ILE C 25 O ALA C 38 SHEET 3 F 7 ILE C 4 ASP C 10 -1 N ALA C 6 O ASP C 28 SHEET 4 F 7 GLY C 209 SER C 215 -1 O ILE C 210 N LEU C 9 SHEET 5 F 7 TRP C 88 SER C 96 -1 N SER C 94 O ALA C 211 SHEET 6 F 7 VAL C 170 PHE C 175 -1 O PHE C 175 N VAL C 91 SHEET 7 F 7 LEU C 140 GLY C 144 -1 N ILE C 141 O LEU C 174 SHEET 1 G 6 LYS C 36 LYS C 39 0 SHEET 2 G 6 HIS C 24 ILE C 29 -1 N ILE C 25 O ALA C 38 SHEET 3 G 6 ILE C 4 ASP C 10 -1 N ALA C 6 O ASP C 28 SHEET 4 G 6 GLY C 209 SER C 215 -1 O ILE C 210 N LEU C 9 SHEET 5 G 6 TRP C 88 SER C 96 -1 N SER C 94 O ALA C 211 SHEET 6 G 6 VAL C 179 HIS C 180 -1 O VAL C 179 N VAL C 89
LINK CA CA A 238 OD2 ASP A 10 1555 1555 2.43 LINK CA CA A 238 O TYR A 12 1555 1555 2.31 LINK CA CA A 238 OD1 ASN A 14 1555 1555 2.35 LINK CA CA A 238 OD2 ASP A 19 1555 1555 2.35 LINK MN MN A 239 OE1 GLU A 8 1555 1555 2.17 LINK MN MN A 239 OD2 ASP A 10 1555 1555 2.08 LINK MN MN A 239 OD1 ASP A 19 1555 1555 2.25 LINK MN MN A 239 NE2 HIS A 24 1555 1555 2.21 LINK CA CA C 238 OD1 ASP C 10 1555 1555 2.45 LINK CA CA C 238 O TYR C 12 1555 1555 2.34 LINK CA CA C 238 OD1 ASN C 14 1555 1555 2.30 LINK CA CA C 238 OD2 ASP C 19 1555 1555 2.41 LINK MN MN C 239 OE1 GLU C 8 1555 1555 2.14 LINK MN MN C 239 OD2 ASP C 10 1555 1555 2.18 LINK MN MN C 239 OD1 ASP C 19 1555 1555 2.30 LINK MN MN C 239 NE2 HIS C 24 1555 1555 2.25 LINK CA CA A 238 O HOH A 562 1555 1555 2.39 LINK CA CA A 238 OD1 ASP A 10 1555 1555 2.49 LINK CA CA A 238 O HOH A 479 1555 1555 2.31 LINK MN MN A 239 O HOH A 483 1555 1555 2.38 LINK MN MN A 239 O HOH A 551 1555 1555 2.09 LINK CA CA C 238 O HOH C 520 1555 1555 2.39 LINK CA CA C 238 OD2 ASP C 10 1555 1555 2.41 LINK CA CA C 238 O HOH C 500 1555 1555 2.31 LINK MN MN C 239 O HOH C 524 1555 1555 2.07 LINK MN MN C 239 O HOH C 566 1555 1555 2.10
CISPEP 1 GLY A 149 THR A 150 0 2.03 CISPEP 2 ALA A 207 ASP A 208 0 2.32 CISPEP 3 GLY C 149 THR C 150 0 5.65 CISPEP 4 ALA C 207 ASP C 208 0 -0.27
SITE 1 AC1 11 TYR A 12 ASN A 14 PRO A 68 ASN A 69 SITE 2 AC1 11 GLY A 98 LEU A 99 TYR A 100 ALA A 207 SITE 3 AC1 11 ASP A 208 GLY A 227 ARG A 228 SITE 1 AC2 11 TYR C 12 ASN C 14 PRO C 68 GLY C 98 SITE 2 AC2 11 LEU C 99 TYR C 100 ALA C 207 ASP C 208 SITE 3 AC2 11 GLY C 227 ARG C 228 HOH C 495 SITE 1 AC3 6 ASP A 10 TYR A 12 ASN A 14 ASP A 19 SITE 2 AC3 6 HOH A 479 HOH A 562 SITE 1 AC4 6 ASP C 10 TYR C 12 ASN C 14 ASP C 19 SITE 2 AC4 6 HOH C 500 HOH C 520 SITE 1 AC5 6 GLU C 8 ASP C 10 ASP C 19 HIS C 24 SITE 2 AC5 6 HOH C 524 HOH C 566 SITE 1 AC6 6 GLU A 8 ASP A 10 ASP A 19 HIS A 24 SITE 2 AC6 6 HOH A 483 HOH A 551
CRYST1 67.033 97.332 71.086 90.00 90.00 90.00 P 21 21 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 0.014918 0.000000 0.000000 0.00000
SCALE2 0.000000 0.010274 0.000000 0.00000
SCALE3 0.000000 0.000000 0.014067 0.00000