PDB Short entry for 2ZBJ HEADER SUGAR BINDING PROTEIN 22-OCT-07 2ZBJ TITLE CRYSTAL STRUCTURE OF DIOCLEA ROSTRATA LECTIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: LECTIN ALPHA CHAIN; COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: DIOCLEA ROSTRATA; SOURCE 3 ORGANISM_TAXID: 192416; SOURCE 4 TISSUE: SEED; SOURCE 5 OTHER_DETAILS: SEED LECTIN KEYWDS LEGUMINOSAE, LECTIN, DIOCLEINAE, DIOCLEA ROSTRATA, CALCIUM, KEYWDS 2 MANGANESE, METAL-BINDING, VACUOLE, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.M.DE OLIVEIRA,P.DELATORRE,B.A.M.DA ROCHA,E.P.DE SOUSA, AUTHOR 2 K.S.NASCIMENTO,G.A.BEZERRA,T.R.MOURA,R.G.BENEVIDES,E.H.S.BEZERRA, AUTHOR 3 F.B.M.B.MORENO,V.N.FREIRE,W.F.DE AZEVEDO JR.,B.S.CAVADA REVDAT 4 01-NOV-23 2ZBJ 1 REMARK LINK REVDAT 3 24-FEB-09 2ZBJ 1 VERSN REVDAT 2 28-OCT-08 2ZBJ 1 JRNL REVDAT 1 19-AUG-08 2ZBJ 0 JRNL AUTH T.M.DE OLIVEIRA,P.DELATORRE,B.A.M.DA ROCHA,E.P.DE SOUZA, JRNL AUTH 2 K.S.NASCIMENTO,G.A.BEZERRA,T.R.MOURA,R.G.BENEVIDES, JRNL AUTH 3 E.H.S.BEZERRA,F.B.M.B.MORENO,V.N.FREIRE,W.F.DE AZEVEDO JR., JRNL AUTH 4 B.S.CAVADA JRNL TITL CRYSTAL STRUCTURE OF DIOCLEA ROSTRATA LECTIN: INSIGHTS INTO JRNL TITL 2 UNDERSTANDING THE PH-DEPENDENT DIMER-TETRAMER EQUILIBRIUM JRNL TITL 3 AND THE STRUCTURAL BASIS FOR CARBOHYDRATE RECOGNITION IN JRNL TITL 4 DIOCLEINAE LECTINS JRNL REF J.STRUCT.BIOL. V. 164 177 2008 JRNL REFN ISSN 1047-8477 JRNL PMID 18682294 JRNL DOI 10.1016/J.JSB.2008.05.012 REMARK 2 REMARK 2 RESOLUTION. 2.05 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) : 2.05 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 14526 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) : 0.189 REMARK 3 R VALUE (WORKING SET) : 0.187 REMARK 3 FREE R VALUE : 0.238 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 766 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) : 2.05 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.10 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1063 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2390 REMARK 3 BIN FREE R VALUE SET COUNT : 66 REMARK 3 BIN FREE R VALUE : 0.3170 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1764 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 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) : 25.31 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.200 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.170 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.130 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.830 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.936 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1815 ; 0.020 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2476 ; 1.986 ; 1.950 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 230 ; 7.974 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 75 ;37.640 ;24.660 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 277 ;17.189 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;19.227 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 285 ; 0.130 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1380 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 863 ; 0.238 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1257 ; 0.312 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 139 ; 0.237 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 3 ; 0.121 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 61 ; 0.267 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 11 ; 0.481 ; 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): 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 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 2ZBJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-OCT-07. REMARK 100 THE DEPOSITION ID IS D_1000027763. 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 : 7.5-8.5 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) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MAR CCD 165 MM REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14526 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 33.150 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 9.400 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 2.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.10 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.34100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.100 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 1H9W REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.29 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M NA-HEPES PH 7.5-8.5, 0.4-1.2M REMARK 280 SODIUM POTASSIUM TARTRATE, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293K 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 30.75550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 44.11000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 43.88200 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 30.75550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 44.11000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 43.88200 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 30.75550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 44.11000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 43.88200 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 30.75550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 44.11000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 43.88200 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: 8420 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 32470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -133.0 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 61.51100 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 88.22000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -1.000000 0.000000 0.000000 61.51100 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 88.22000 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 266 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 291 LIES ON A SPECIAL POSITION. 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 ASN A 118 REMARK 465 SER A 119 REMARK 465 ILE A 120 REMARK 465 ALA A 121 REMARK 465 ASP A 122 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 VAL A 50 CG1 CG2 REMARK 470 THR A 68 OG1 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 282 O HOH A 368 1.67 REMARK 500 CD2 LEU A 230 O HOH A 332 1.91 REMARK 500 O HOH A 320 O HOH A 367 2.04 REMARK 500 OE1 GLU A 87 O HOH A 360 2.09 REMARK 500 C THR A 117 O HOH A 355 2.11 REMARK 500 OD1 ASP A 218 O HOH A 328 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 O HOH A 274 O HOH A 306 6554 1.60 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 ARG A 204 CG ARG A 204 CD 0.160 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 ARG A 172 NE - CZ - NH2 ANGL. DEV. = -5.0 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 21 47.20 -84.48 REMARK 500 VAL A 84 -54.47 -122.38 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 238 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 8 OE2 REMARK 620 2 ASP A 10 OD2 89.6 REMARK 620 3 ASP A 19 OD1 167.9 96.4 REMARK 620 4 HOH A 352 O 92.8 84.5 77.5 REMARK 620 5 HOH A 353 O 88.5 175.2 86.2 99.9 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 239 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 10 OD1 REMARK 620 2 ASP A 10 OD2 51.8 REMARK 620 3 TYR A 12 O 73.9 115.6 REMARK 620 4 ASN A 14 OD1 146.5 161.6 79.8 REMARK 620 5 ASP A 19 OD2 109.4 82.1 86.7 89.1 REMARK 620 6 HOH A 323 O 110.7 70.3 174.1 94.5 94.8 REMARK 620 7 HOH A 333 O 68.9 99.3 89.2 90.6 175.9 89.3 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 PO4 A1285 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 238 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 239 DBREF 2ZBJ A 1 237 UNP P58908 LECA_DIORO 1 237 SEQRES 1 A 237 ALA ASP THR ILE VAL ALA VAL GLU LEU ASP SER TYR PRO SEQRES 2 A 237 ASN THR ASP ILE GLY ASP PRO ASN TYR PRO HIS ILE GLY SEQRES 3 A 237 ILE ASP ILE LYS SER ILE ARG SER LYS SER THR ALA ARG SEQRES 4 A 237 TRP ASN MET GLN THR GLY LYS VAL GLY THR VAL HIS ILE SEQRES 5 A 237 SER TYR ASN SER VAL ALA LYS ARG LEU SER ALA VAL VAL SEQRES 6 A 237 SER TYR THR GLY SER SER SER THR THR VAL SER TYR ASP SEQRES 7 A 237 VAL ASP LEU ASN ASN VAL LEU PRO GLU TRP VAL ARG VAL SEQRES 8 A 237 GLY LEU SER ALA THR THR GLY LEU TYR LYS GLU THR ASN SEQRES 9 A 237 THR ILE LEU SER TRP SER PHE THR SER LYS LEU LYS THR SEQRES 10 A 237 ASN SER ILE ALA ASP ALA ASN SER LEU HIS PHE THR PHE SEQRES 11 A 237 ASN GLN PHE SER GLN ASN PRO LYS ASP LEU ILE LEU GLN SEQRES 12 A 237 GLY ASP ALA THR THR ASP SER ASP GLY ASN LEU GLU LEU SEQRES 13 A 237 THR LYS VAL SER SER SER GLY ASP PRO GLN GLY ASN SER SEQRES 14 A 237 VAL GLY ARG ALA LEU PHE TYR ALA PRO VAL HIS ILE TRP SEQRES 15 A 237 GLU LYS SER ALA VAL VAL ALA SER PHE ASP ALA THR PHE SEQRES 16 A 237 THR PHE LEU ILE LYS SER PRO ASP ARG ASP PRO ALA ASP SEQRES 17 A 237 GLY ILE THR PHE PHE ILE ALA ASN PRO ASP THR SER ILE SEQRES 18 A 237 PRO SER GLY SER GLY GLY ARG LEU LEU GLY LEU PHE PRO SEQRES 19 A 237 ASP ALA ASN HET PO4 A1285 5 HET MN A 238 1 HET CA A 239 1 HETNAM PO4 PHOSPHATE ION HETNAM MN MANGANESE (II) ION HETNAM CA CALCIUM ION FORMUL 2 PO4 O4 P 3- FORMUL 3 MN MN 2+ FORMUL 4 CA CA 2+ FORMUL 5 HOH *102(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 GLY A 226 LEU A 230 5 5 SHEET 1 A 7 SER A 36 ARG A 39 0 SHEET 2 A 7 HIS A 24 ILE A 29 -1 N ILE A 27 O SER A 36 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 ALA A 215 -1 O ILE A 210 N LEU A 9 SHEET 5 A 7 TRP A 88 THR A 96 -1 N SER A 94 O THR A 211 SHEET 6 A 7 VAL A 170 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 SER A 36 ARG A 39 0 SHEET 2 B 6 HIS A 24 ILE A 29 -1 N ILE A 27 O SER A 36 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 ALA A 215 -1 O ILE A 210 N LEU A 9 SHEET 5 B 6 TRP A 88 THR A 96 -1 N SER A 94 O THR 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 THR A 73 ASP A 78 0 SHEET 2 C 6 ARG A 60 TYR A 67 -1 N VAL A 65 O THR A 73 SHEET 3 C 6 VAL A 47 ASN A 55 -1 N SER A 53 O SER A 62 SHEET 4 C 6 VAL A 188 LEU A 198 -1 O PHE A 197 N GLY A 48 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 PHE A 130 N TRP A 109 SHEET 1 D 7 THR A 73 ASP A 78 0 SHEET 2 D 7 ARG A 60 TYR A 67 -1 N VAL A 65 O THR A 73 SHEET 3 D 7 VAL A 47 ASN A 55 -1 N SER A 53 O SER A 62 SHEET 4 D 7 VAL A 188 LEU A 198 -1 O PHE A 197 N GLY A 48 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 GLU 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 GLU A 155 LINK OE2 GLU A 8 MN MN A 238 1555 1555 2.31 LINK OD2 ASP A 10 MN MN A 238 1555 1555 2.17 LINK OD1 ASP A 10 CA CA A 239 1555 1555 2.44 LINK OD2 ASP A 10 CA CA A 239 1555 1555 2.55 LINK O TYR A 12 CA CA A 239 1555 1555 2.27 LINK OD1 ASN A 14 CA CA A 239 1555 1555 2.43 LINK OD1 ASP A 19 MN MN A 238 1555 1555 2.37 LINK OD2 ASP A 19 CA CA A 239 1555 1555 2.32 LINK MN MN A 238 O HOH A 352 1555 1555 2.05 LINK MN MN A 238 O HOH A 353 1555 1555 2.21 LINK CA CA A 239 O HOH A 323 1555 1555 2.31 LINK CA CA A 239 O HOH A 333 1555 1555 2.45 CISPEP 1 ALA A 207 ASP A 208 0 0.83 SITE 1 AC1 6 ASN A 14 SER A 71 GLY A 98 ASP A 208 SITE 2 AC1 6 GLY A 227 ARG A 228 SITE 1 AC2 6 GLU A 8 ASP A 10 ASP A 19 HIS A 24 SITE 2 AC2 6 HOH A 352 HOH A 353 SITE 1 AC3 6 ASP A 10 TYR A 12 ASN A 14 ASP A 19 SITE 2 AC3 6 HOH A 323 HOH A 333 CRYST1 61.511 88.220 87.764 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 0.016257 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011335 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011394 0.00000