HEADER SUGAR BINDING PROTEIN 12-JAN-17 5MU9 TITLE MOA-E-64 COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: AGGLUTININ; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MARASMIUS OREADES; SOURCE 3 ORGANISM_TAXID: 181124; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 5 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 7 EXPRESSION_SYSTEM_PLASMID: PT7-LO KEYWDS PAPAIN-LIKE PROTEASE, E-64 INHIBITOR COMPLEX, LECTIN, CALCIUM- KEYWDS 2 BINDING, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR G.CORDARA,D.MANNA,U.KRENGEL REVDAT 5 17-JAN-24 5MU9 1 HETSYN LINK REVDAT 4 29-JUL-20 5MU9 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 13-SEP-17 5MU9 1 JRNL REVDAT 2 30-AUG-17 5MU9 1 JRNL REVDAT 1 12-JUL-17 5MU9 0 JRNL AUTH G.CORDARA,D.MANNA,U.KRENGEL JRNL TITL FAMILY OF PAPAIN-LIKE FUNGAL CHIMEROLECTINS WITH DISTINCT JRNL TITL 2 CA(2+)-DEPENDENT ACTIVATION MECHANISM. JRNL REF BIOCHEMISTRY V. 56 4689 2017 JRNL REFN ISSN 1520-4995 JRNL PMID 28665586 JRNL DOI 10.1021/ACS.BIOCHEM.7B00317 REMARK 2 REMARK 2 RESOLUTION. 1.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0135 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.38 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 3 NUMBER OF REFLECTIONS : 94423 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) : 0.148 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.183 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4970 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) : 1.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.33 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4614 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 63.19 REMARK 3 BIN R VALUE (WORKING SET) : 0.2650 REMARK 3 BIN FREE R VALUE SET COUNT : 243 REMARK 3 BIN FREE R VALUE : 0.3000 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2277 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 136 REMARK 3 SOLVENT ATOMS : 333 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 13.17 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.23000 REMARK 3 B22 (A**2) : 0.23000 REMARK 3 B33 (A**2) : -0.75000 REMARK 3 B12 (A**2) : 0.12000 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): 0.040 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.043 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.030 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.400 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.972 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.960 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2621 ; 0.025 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 2317 ; 0.003 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3602 ; 2.278 ; 1.973 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5380 ; 1.450 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 325 ; 7.197 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 122 ;38.513 ;24.836 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 372 ;12.071 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 7 ;20.221 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 399 ; 0.455 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2989 ; 0.014 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 647 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1214 ; 1.556 ; 1.023 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1212 ; 1.543 ; 1.552 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1524 ; 1.780 ; 1.548 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1525 ; 1.780 ; 6.978 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1407 ; 2.812 ; 4.037 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1408 ; 2.811 ; 4.035 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2064 ; 2.949 ;64.184 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3254 ; 3.296 ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3077 ; 2.603 ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 2488 ; 5.634 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 2402 ;10.907 ; 5.000 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 : NULL 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 5MU9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 12-JAN-17. REMARK 100 THE DEPOSITION ID IS D_1200003029. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-OCT-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.8726 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS VERSION SEPTEMBER 26, 2012 REMARK 200 DATA SCALING SOFTWARE : XDS VERSION SEPTEMBER 26, 2012 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 99395 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.300 REMARK 200 RESOLUTION RANGE LOW (A) : 46.380 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.2 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.07000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 14.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.38 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.80 REMARK 200 R MERGE FOR SHELL (I) : 0.50000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER 2.5.1 REMARK 200 STARTING MODEL: 3EF2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 62.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.26 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M IMIDAZOLE PH 8.0, 15% PEG 8000, REMARK 280 7.5% DMSO AND 0.2 M CALCIUM ACETATE, VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 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 49.92550 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 49.92550 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 49.92550 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 49.92550 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 49.92550 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 49.92550 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11010 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 22590 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -120.93400 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 -49.92550 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 579 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 MET A 1 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 NZ LYS A 134 O HOH A 401 1.49 REMARK 500 O PRO A 204 O HOH A 402 1.90 REMARK 500 O HOH A 679 O HOH A 716 2.10 REMARK 500 O HOH A 402 O HOH A 622 2.14 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 169 CZ ARG A 169 NH1 0.091 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 4 NE - CZ - NH1 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 4 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 169 CD - NE - CZ ANGL. DEV. = 9.3 DEGREES REMARK 500 ARG A 169 NE - CZ - NH1 ANGL. DEV. = 6.3 DEGREES REMARK 500 ARG A 169 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ARG A 169 NE - CZ - NH2 ANGL. DEV. = -8.7 DEGREES REMARK 500 ARG A 169 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 ARG A 178 NE - CZ - NH2 ANGL. DEV. = -3.4 DEGREES REMARK 500 TYR A 180 CB - CG - CD1 ANGL. DEV. = -3.6 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 75 19.78 52.99 REMARK 500 THR A 109 -52.13 -121.22 REMARK 500 HIS A 172 51.12 -116.24 REMARK 500 GLN A 211 -43.85 64.25 REMARK 500 TYR A 213 73.21 -155.07 REMARK 500 ASP A 214 -165.98 -117.27 REMARK 500 ASN A 277 -1.78 -147.44 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 733 DISTANCE = 6.27 ANGSTROMS 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 314 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LEU A 182 O REMARK 620 2 ASP A 183 OD1 82.9 REMARK 620 3 ASP A 214 OD2 61.2 84.1 REMARK 620 4 ASP A 216 OD1 59.8 85.2 1.8 REMARK 620 5 E64 A 312 O4 54.4 85.2 7.0 5.5 REMARK 620 6 HOH A 656 O 58.3 89.8 6.8 5.1 5.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 313 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 183 OD1 REMARK 620 2 ASP A 183 OD2 52.6 REMARK 620 3 GLN A 211 O 126.1 90.2 REMARK 620 4 ASP A 214 OD1 122.4 83.3 7.3 REMARK 620 5 ASP A 216 OD2 120.0 83.7 6.7 4.3 REMARK 620 6 ASP A 217 OD2 128.0 88.9 4.6 5.9 8.1 REMARK 620 7 HOH A 432 O 126.3 92.8 3.6 10.7 9.1 7.9 REMARK 620 N 1 2 3 4 5 6 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 315 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN A 276 O REMARK 620 2 HOH A 402 O 144.7 REMARK 620 3 HOH A 427 O 57.8 97.1 REMARK 620 4 HOH A 580 O 90.0 109.5 77.1 REMARK 620 5 HOH A 622 O 90.1 56.6 72.3 143.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 316 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 552 O REMARK 620 2 HOH A 571 O 89.1 REMARK 620 3 HOH A 607 O 64.0 101.2 REMARK 620 4 HOH A 637 O 59.1 138.5 88.6 REMARK 620 5 HOH A 644 O 136.2 91.0 157.1 95.0 REMARK 620 6 FUC D 2 O2 138.8 83.0 77.9 138.5 84.5 REMARK 620 7 FUC D 2 O3 120.3 147.5 82.0 73.5 77.5 65.9 REMARK 620 N 1 2 3 4 5 6 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3EF2 RELATED DB: PDB REMARK 900 LIGAND-FREE PROTEIN REMARK 900 RELATED ID: 2IHO RELATED DB: PDB REMARK 900 CALCIUM- AND LIGAND-FREE PROTEIN REMARK 900 RELATED ID: 5D61 RELATED DB: PDB REMARK 900 PROTEIN BOUND TO THE Z-VAD-FMK INHIBITOR REMARK 900 RELATED ID: 5D62 RELATED DB: PDB REMARK 900 PROTEIN BOUND TO THE Z-VAD-FMK INHIBITOR REMARK 900 RELATED ID: 5D63 RELATED DB: PDB REMARK 900 PROTEIN BOUND TO THE Z-VAD-FMK INHIBITOR DBREF 5MU9 A 1 293 UNP Q8X123 Q8X123_9AGAR 1 293 SEQADV 5MU9 ALA A 63 UNP Q8X123 CYS 63 ENGINEERED MUTATION SEQRES 1 A 293 MET SER LEU ARG ARG GLY ILE TYR HIS ILE GLU ASN ALA SEQRES 2 A 293 GLY VAL PRO SER ALA ILE ASP LEU LYS ASP GLY SER SER SEQRES 3 A 293 SER ASP GLY THR PRO ILE VAL GLY TRP GLN PHE THR PRO SEQRES 4 A 293 ASP THR ILE ASN TRP HIS GLN LEU TRP LEU ALA GLU PRO SEQRES 5 A 293 ILE PRO ASN VAL ALA ASP THR PHE THR LEU ALA ASN LEU SEQRES 6 A 293 PHE SER GLY THR TYR MET ASP LEU TYR ASN GLY SER SER SEQRES 7 A 293 GLU ALA GLY THR ALA VAL ASN GLY TRP GLN GLY THR ALA SEQRES 8 A 293 PHE THR THR ASN PRO HIS GLN LEU TRP THR ILE LYS LYS SEQRES 9 A 293 SER SER ASP GLY THR SER TYR LYS ILE GLN ASN TYR GLY SEQRES 10 A 293 SER LYS THR PHE VAL ASP LEU VAL ASN GLY ASP SER SER SEQRES 11 A 293 ASP GLY ALA LYS ILE ALA GLY TRP THR GLY THR TRP ASP SEQRES 12 A 293 GLU GLY ASN PRO HIS GLN LYS TRP TYR PHE ASN ARG MET SEQRES 13 A 293 SER VAL SER SER ALA GLU ALA GLN ALA ALA ILE ALA ARG SEQRES 14 A 293 ASN PRO HIS ILE HIS GLY THR TYR ARG GLY TYR ILE LEU SEQRES 15 A 293 ASP GLY GLU TYR LEU VAL LEU PRO ASN ALA THR PHE THR SEQRES 16 A 293 GLN ILE TRP LYS ASP SER GLY LEU PRO GLY SER LYS TRP SEQRES 17 A 293 ARG GLU GLN ILE TYR ASP CYS ASP ASP PHE ALA ILE ALA SEQRES 18 A 293 MET LYS ALA ALA VAL GLY LYS TRP GLY ALA ASP SER TRP SEQRES 19 A 293 LYS ALA ASN GLY PHE ALA ILE PHE CYS GLY VAL MET LEU SEQRES 20 A 293 GLY VAL ASN LYS ALA GLY ASP ALA ALA HIS ALA TYR ASN SEQRES 21 A 293 PHE THR LEU THR LYS ASP HIS ALA ASP ILE VAL PHE PHE SEQRES 22 A 293 GLU PRO GLN ASN GLY GLY TYR LEU ASN ASP ILE GLY TYR SEQRES 23 A 293 ASP SER TYR MET ALA PHE TYR HET GAL B 1 12 HET FUC B 2 10 HET GLA B 3 11 HET GLA C 1 12 HET FUC C 2 10 HET GLA C 3 11 HET GLA D 1 12 HET FUC D 2 10 HET GLA D 3 11 HET EDO A 310 4 HET ACT A 311 4 HET E64 A 312 36 HET CA A 313 1 HET CA A 314 1 HET NA A 315 1 HET CA A 316 1 HETNAM GAL BETA-D-GALACTOPYRANOSE HETNAM FUC ALPHA-L-FUCOPYRANOSE HETNAM GLA ALPHA-D-GALACTOPYRANOSE HETNAM EDO 1,2-ETHANEDIOL HETNAM ACT ACETATE ION HETNAM E64 N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO- HETNAM 2 E64 BUTYL]-GUANIDINE HETNAM CA CALCIUM ION HETNAM NA SODIUM ION HETSYN GAL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE HETSYN FUC ALPHA-L-FUCOSE; 6-DEOXY-ALPHA-L-GALACTOPYRANOSE; L- HETSYN 2 FUC FUCOSE; FUCOSE HETSYN GLA ALPHA-D-GALACTOSE; D-GALACTOSE; GALACTOSE; ALPHA D- HETSYN 2 GLA GALACTOSE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 GAL C6 H12 O6 FORMUL 2 FUC 3(C6 H12 O5) FORMUL 2 GLA 5(C6 H12 O6) FORMUL 5 EDO C2 H6 O2 FORMUL 6 ACT C2 H3 O2 1- FORMUL 7 E64 C15 H30 N5 O5 1+ FORMUL 8 CA 3(CA 2+) FORMUL 10 NA NA 1+ FORMUL 12 HOH *333(H2 O) HELIX 1 AA1 ASP A 23 SER A 25 5 3 HELIX 2 AA2 ASN A 75 SER A 77 5 3 HELIX 3 AA3 ASN A 95 GLN A 98 5 4 HELIX 4 AA4 ASN A 126 ASP A 128 5 3 HELIX 5 AA5 ASN A 146 GLN A 149 5 4 HELIX 6 AA6 SER A 160 ARG A 169 1 10 HELIX 7 AA7 PRO A 190 SER A 201 1 12 HELIX 8 AA8 GLY A 202 SER A 206 5 5 HELIX 9 AA9 ASP A 214 TRP A 234 1 21 SHEET 1 A 4 TRP A 151 ARG A 155 0 SHEET 2 A 4 GLY A 6 ASN A 12 -1 SHEET 3 A 4 LEU A 47 PRO A 52 -1 SHEET 4 A 4 PHE A 60 ASN A 64 -1 SHEET 1 B 2 ALA A 18 LEU A 21 0 SHEET 2 B 2 ILE A 32 TRP A 35 -1 SHEET 1 C 2 TYR A 70 LEU A 73 0 SHEET 2 C 2 VAL A 84 TRP A 87 -1 SHEET 1 D 2 TRP A 100 LYS A 104 0 SHEET 2 D 2 TYR A 111 ASN A 115 -1 SHEET 1 E 2 PHE A 121 LEU A 124 0 SHEET 2 E 2 ILE A 135 TRP A 138 -1 SHEET 1 F 2 SER A 157 SER A 159 0 SHEET 2 F 2 GLU A 185 LEU A 187 -1 SHEET 1 G 6 ARG A 178 TYR A 180 0 SHEET 2 G 6 ASP A 287 PHE A 292 1 SHEET 3 G 6 GLY A 244 VAL A 249 -1 SHEET 4 G 6 ALA A 256 LEU A 263 -1 SHEET 5 G 6 ILE A 270 GLU A 274 -1 SHEET 6 G 6 GLY A 279 LEU A 281 -1 LINK SG CYS A 215 C2 E64 A 312 1555 1555 1.92 LINK O2 GAL B 1 C1 FUC B 2 1555 1555 1.39 LINK O3 GAL B 1 C1 GLA B 3 1555 1555 1.45 LINK O2 GLA C 1 C1 FUC C 2 1555 1555 1.41 LINK O3 GLA C 1 C1 GLA C 3 1555 1555 1.44 LINK O2 GLA D 1 C1 FUC D 2 1555 1555 1.46 LINK O3 GLA D 1 C1 GLA D 3 1555 1555 1.39 LINK O LEU A 182 CA CA A 314 1555 11454 2.24 LINK OD1 ASP A 183 CA CA A 313 1555 11454 2.59 LINK OD2 ASP A 183 CA CA A 313 1555 11454 2.49 LINK OD1 ASP A 183 CA CA A 314 1555 11454 2.33 LINK O GLN A 211 CA CA A 313 1555 1555 2.34 LINK OD1 ASP A 214 CA CA A 313 1555 1555 2.39 LINK OD2 ASP A 214 CA CA A 314 1555 1555 2.33 LINK OD2 ASP A 216 CA CA A 313 1555 1555 2.39 LINK OD1 ASP A 216 CA CA A 314 1555 1555 2.33 LINK OD2 ASP A 217 CA CA A 313 1555 1555 2.39 LINK O GLN A 276 NA NA A 315 1555 1555 2.18 LINK O4 E64 A 312 CA CA A 314 1555 1555 2.33 LINK CA CA A 313 O HOH A 432 1555 1555 2.44 LINK CA CA A 314 O HOH A 656 1555 1555 2.37 LINK NA NA A 315 O HOH A 402 1555 1555 2.45 LINK NA NA A 315 O HOH A 427 1555 1555 3.00 LINK NA NA A 315 O HOH A 580 1555 1555 2.14 LINK NA NA A 315 O HOH A 622 1555 1555 1.99 LINK CA CA A 316 O HOH A 552 1555 10555 2.32 LINK CA CA A 316 O HOH A 571 1555 1555 2.51 LINK CA CA A 316 O HOH A 607 1555 10555 2.33 LINK CA CA A 316 O HOH A 637 1555 1555 2.35 LINK CA CA A 316 O HOH A 644 1555 1555 2.14 LINK CA CA A 316 O2 FUC D 2 1555 1555 2.44 LINK CA CA A 316 O3 FUC D 2 1555 1555 2.68 CRYST1 120.934 120.934 99.851 90.00 90.00 120.00 P 63 2 2 12 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 0.008269 0.004774 0.000000 0.00000 SCALE2 0.000000 0.009548 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010015 0.00000