PDB Short entry for 3ARQ HEADER HYDROLASE/HYDROLASE INHIBITOR 09-DEC-10 3ARQ TITLE CRYSTAL STRUCTURE ANALYSIS OF CHITINASE A FROM VIBRIO HARVEYI WITH TITLE 2 NOVEL INHIBITORS - COMPLEX STRUCTURE WITH IDARUBICIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: CHITINASE A; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 22-597; COMPND 5 EC: 3.2.1.14; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO HARVEYI; SOURCE 3 ORGANISM_TAXID: 669; SOURCE 4 STRAIN: LMG7890; SOURCE 5 GENE: CHIA; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: M15; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PQE60 KEYWDS TIM BARREL, INHIBITOR COMPLEX, GLYCOSIDASE, HYDROLASE, HYDROLASE- KEYWDS 2 HYDROLASE INHIBITOR COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR S.PANTOOM,I.R.VETTER,H.PRINZ,W.SUGINTA REVDAT 3 01-NOV-23 3ARQ 1 REMARK SEQADV REVDAT 2 29-JAN-14 3ARQ 1 JRNL VERSN REVDAT 1 20-APR-11 3ARQ 0 JRNL AUTH S.PANTOOM,I.R.VETTER,H.PRINZ,W.SUGINTA JRNL TITL POTENT FAMILY-18 CHITINASE INHIBITORS: X-RAY STRUCTURES, JRNL TITL 2 AFFINITIES, AND BINDING MECHANISMS JRNL REF J.BIOL.CHEM. V. 286 24312 2011 JRNL REFN ISSN 0021-9258 JRNL PMID 21531720 JRNL DOI 10.1074/JBC.M110.183376 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH C.SONGSIRIRITTHIGUL,S.PANTOOM,A.H.AGUDA,R.C.ROBINSON, REMARK 1 AUTH 2 W.SUGINTA REMARK 1 TITL CRYSTAL STRUCTURES OF VIBRIO HARVEYI CHITINASE A COMPLEXED REMARK 1 TITL 2 WITH CHITOOLIGOSACCHARIDES: IMPLICATIONS FOR THE CATALYTIC REMARK 1 TITL 3 MECHANISM REMARK 1 REF J.STRUCT.BIOL. V. 162 491 2008 REMARK 1 REFN ISSN 1047-8477 REMARK 1 PMID 18467126 REMARK 1 DOI 10.1016/J.JSB.2008.03.008 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.6.0093 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) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.93 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 96141 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) : 0.147 REMARK 3 R VALUE (WORKING SET) : 0.145 REMARK 3 FREE R VALUE : 0.184 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4807 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) : 1.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.54 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6437 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.1700 REMARK 3 BIN FREE R VALUE SET COUNT : 342 REMARK 3 BIN FREE R VALUE : 0.2190 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4405 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 826 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 14.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.14000 REMARK 3 B22 (A**2) : 0.22000 REMARK 3 B33 (A**2) : -0.03000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.12000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.069 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.040 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.037 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.953 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4815 ; 0.029 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6613 ; 2.335 ; 1.960 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 640 ; 6.337 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 220 ;37.495 ;25.273 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 736 ;11.871 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;16.180 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 695 ; 0.163 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3798 ; 0.014 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 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 USED IF PRESENT IN REMARK 3 THE INPUT U VALUES: REFINED INDIVIDUALLY REMARK 4 REMARK 4 3ARQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 27-DEC-10. REMARK 100 THE DEPOSITION ID IS D_1000029613. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-APR-09 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X10SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.87312 REMARK 200 MONOCHROMATOR : SI(111) MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 96142 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 19.928 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : 0.07200 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.4800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.54 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.9 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.49300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 6.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: 3B9A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 48.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.39 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 16%(W/V) PEG 4000, 21%(V/V) PROPANOL, REMARK 280 0.1M NA-ACETATE, PH 5.6, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 25.44500 REMARK 290 SMTRY3 2 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 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 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 ARG A 597 REMARK 465 ARG A 598 REMARK 465 SER A 599 REMARK 465 HIS A 600 REMARK 465 HIS A 601 REMARK 465 HIS A 602 REMARK 465 HIS A 603 REMARK 465 HIS A 604 REMARK 465 HIS A 605 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 835 O HOH A 859 1.55 REMARK 500 O HOH A 811 O HOH A 912 1.65 REMARK 500 SD MET A 480 O HOH A 643 1.69 REMARK 500 O HOH A 837 O HOH A 1095 1.70 REMARK 500 CE MET A 480 O HOH A 643 1.71 REMARK 500 CG MET A 480 O HOH A 643 1.76 REMARK 500 O HOH A 688 O HOH A 1361 1.78 REMARK 500 O HOH A 1330 O HOH A 1389 1.79 REMARK 500 O HOH A 843 O HOH A 1102 1.84 REMARK 500 O HOH A 840 O HOH A 942 1.85 REMARK 500 O HOH A 987 O HOH A 1280 1.85 REMARK 500 O TYR A 31 O HOH A 693 1.87 REMARK 500 O HOH A 839 O HOH A 1039 1.88 REMARK 500 OH TYR A 435 O HOH A 805 1.90 REMARK 500 O HOH A 796 O HOH A 819 1.92 REMARK 500 O HOH A 756 O HOH A 844 1.96 REMARK 500 O HOH A 841 O HOH A 1054 1.99 REMARK 500 O HOH A 620 O HOH A 725 1.99 REMARK 500 O HOH A 814 O HOH A 934 2.00 REMARK 500 O HOH A 735 O HOH A 1041 2.00 REMARK 500 O HOH A 759 O HOH A 1328 2.00 REMARK 500 O HOH A 815 O HOH A 1036 2.02 REMARK 500 O HOH A 818 O HOH A 821 2.04 REMARK 500 O HOH A 731 O HOH A 743 2.06 REMARK 500 O HOH A 831 O HOH A 1285 2.09 REMARK 500 N ASN A 154 O HOH A 814 2.10 REMARK 500 O HOH A 736 O HOH A 769 2.10 REMARK 500 O HOH A 1141 O HOH A 1196 2.11 REMARK 500 O HOH A 656 O HOH A 686 2.12 REMARK 500 O HOH A 662 O HOH A 1080 2.12 REMARK 500 O HOH A 621 O HOH A 1209 2.13 REMARK 500 O HOH A 841 O HOH A 1101 2.14 REMARK 500 O HOH A 762 O HOH A 1252 2.14 REMARK 500 O HOH A 987 O HOH A 1016 2.15 REMARK 500 O HOH A 837 O HOH A 1282 2.16 REMARK 500 O HOH A 820 O HOH A 916 2.17 REMARK 500 O HOH A 1214 O HOH A 1323 2.18 REMARK 500 O HOH A 816 O HOH A 1241 2.18 REMARK 500 O HOH A 730 O HOH A 1190 2.18 REMARK 500 NE1 TRP A 570 O HOH A 775 2.19 REMARK 500 O HOH A 703 O HOH A 1231 2.19 REMARK 500 O HOH A 687 O HOH A 1254 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 688 O HOH A 1382 2556 2.17 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 VAL A 87 CB VAL A 87 CG1 -0.146 REMARK 500 GLU A 466 CB GLU A 466 CG -0.125 REMARK 500 GLU A 542 CD GLU A 542 OE1 0.071 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 173 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 ASP A 183 CB - CG - OD2 ANGL. DEV. = -5.5 DEGREES REMARK 500 LYS A 260 CD - CE - NZ ANGL. DEV. = 14.3 DEGREES REMARK 500 ASP A 279 CB - CG - OD2 ANGL. DEV. = -6.1 DEGREES REMARK 500 PHE A 281 CB - CG - CD2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ARG A 290 NE - CZ - NH1 ANGL. DEV. = 4.4 DEGREES REMARK 500 ARG A 290 NE - CZ - NH2 ANGL. DEV. = -7.5 DEGREES REMARK 500 LYS A 305 CD - CE - NZ ANGL. DEV. = -15.9 DEGREES REMARK 500 ASP A 308 CB - CG - OD2 ANGL. DEV. = 5.7 DEGREES REMARK 500 ARG A 341 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 341 NE - CZ - NH2 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 341 NE - CZ - NH2 ANGL. DEV. = -4.1 DEGREES REMARK 500 LEU A 347 CB - CG - CD1 ANGL. DEV. = -10.7 DEGREES REMARK 500 ASP A 419 CB - CG - OD2 ANGL. DEV. = 7.6 DEGREES REMARK 500 ARG A 463 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 ASP A 475 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 538 NE - CZ - NH1 ANGL. DEV. = -4.2 DEGREES REMARK 500 ASP A 547 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 ASP A 548 CB - CG - OD1 ANGL. DEV. = 5.5 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 ASN A 35 38.27 29.49 REMARK 500 ASN A 35 29.37 39.22 REMARK 500 TYR A 171 -115.31 -92.44 REMARK 500 ASN A 199 35.52 -149.64 REMARK 500 TYR A 223 9.28 82.14 REMARK 500 TYR A 234 -0.58 -150.00 REMARK 500 LYS A 250 -151.95 -133.06 REMARK 500 ASP A 313 76.81 -113.93 REMARK 500 THR A 405 26.28 -145.63 REMARK 500 MET A 460 32.91 -96.98 REMARK 500 MET A 511 -38.15 -134.32 REMARK 500 MET A 511 -38.56 -134.07 REMARK 500 GLU A 531 67.01 62.09 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE DM5 A 606 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 3500 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 3501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 3502 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3ARO RELATED DB: PDB REMARK 900 RELATED ID: 3ARP RELATED DB: PDB REMARK 900 RELATED ID: 3ARR RELATED DB: PDB REMARK 900 RELATED ID: 3ARS RELATED DB: PDB REMARK 900 RELATED ID: 3ART RELATED DB: PDB REMARK 900 RELATED ID: 3ARU RELATED DB: PDB REMARK 900 RELATED ID: 3ARV RELATED DB: PDB REMARK 900 RELATED ID: 3ARW RELATED DB: PDB REMARK 900 RELATED ID: 3ARX RELATED DB: PDB REMARK 900 RELATED ID: 3ARY RELATED DB: PDB REMARK 900 RELATED ID: 3ARZ RELATED DB: PDB REMARK 900 RELATED ID: 3AS0 RELATED DB: PDB REMARK 900 RELATED ID: 3AS1 RELATED DB: PDB REMARK 900 RELATED ID: 3AS2 RELATED DB: PDB REMARK 900 RELATED ID: 3AS3 RELATED DB: PDB DBREF 3ARQ A 22 597 UNP Q9AMP1 Q9AMP1_VIBHA 22 597 SEQADV 3ARQ ARG A 598 UNP Q9AMP1 EXPRESSION TAG SEQADV 3ARQ SER A 599 UNP Q9AMP1 EXPRESSION TAG SEQADV 3ARQ HIS A 600 UNP Q9AMP1 EXPRESSION TAG SEQADV 3ARQ HIS A 601 UNP Q9AMP1 EXPRESSION TAG SEQADV 3ARQ HIS A 602 UNP Q9AMP1 EXPRESSION TAG SEQADV 3ARQ HIS A 603 UNP Q9AMP1 EXPRESSION TAG SEQADV 3ARQ HIS A 604 UNP Q9AMP1 EXPRESSION TAG SEQADV 3ARQ HIS A 605 UNP Q9AMP1 EXPRESSION TAG SEQRES 1 A 584 ALA PRO THR ALA PRO SER ILE ASP MET TYR GLY SER ASN SEQRES 2 A 584 ASN LEU GLN PHE SER LYS ILE GLU LEU ALA MET GLU THR SEQRES 3 A 584 THR SER GLY TYR ASN ASP MET VAL LYS TYR HIS GLU LEU SEQRES 4 A 584 ALA LYS ILE LYS VAL LYS PHE ASN GLN TRP SER GLY THR SEQRES 5 A 584 SER GLY ASP THR TYR ASN VAL TYR PHE ASP GLY VAL LYS SEQRES 6 A 584 VAL ALA THR GLY ALA ILE THR GLY SER GLN THR THR ALA SEQRES 7 A 584 SER PHE GLU TYR GLY GLN GLY GLY LEU TYR GLN MET GLU SEQRES 8 A 584 ILE GLU ALA CYS ASP ALA THR GLY CYS SER LYS SER ALA SEQRES 9 A 584 PRO VAL GLU ILE THR ILE ALA ASP THR ASP GLY SER HIS SEQRES 10 A 584 LEU LYS PRO LEU THR MET ASN VAL ASP PRO ASN ASN LYS SEQRES 11 A 584 SER TYR ASN THR ASP PRO SER ILE VAL MET GLY THR TYR SEQRES 12 A 584 PHE VAL GLU TRP GLY ILE TYR GLY ARG ASP TYR THR VAL SEQRES 13 A 584 ASP ASN MET PRO VAL ASP ASN LEU THR HIS ILE LEU TYR SEQRES 14 A 584 GLY PHE ILE PRO ILE CYS GLY PRO ASN GLU SER VAL LYS SEQRES 15 A 584 SER VAL GLY GLY ASN SER PHE ASN ALA LEU GLN THR ALA SEQRES 16 A 584 CYS ARG GLY VAL ASN ASP TYR GLU VAL VAL ILE HIS ASP SEQRES 17 A 584 PRO TRP ALA ALA TYR GLN LYS SER PHE PRO GLN ALA GLY SEQRES 18 A 584 HIS GLU TYR SER THR PRO ILE LYS GLY ASN TYR ALA MET SEQRES 19 A 584 LEU MET ALA LEU LYS GLN ARG ASN PRO ASP LEU LYS ILE SEQRES 20 A 584 ILE PRO SER ILE GLY GLY TRP THR LEU SER ASP PRO PHE SEQRES 21 A 584 TYR ASP PHE VAL ASP LYS LYS ASN ARG ASP THR PHE VAL SEQRES 22 A 584 ALA SER VAL LYS LYS PHE LEU LYS THR TRP LYS PHE TYR SEQRES 23 A 584 ASP GLY VAL ASP ILE ASP TRP GLU PHE PRO GLY GLY GLY SEQRES 24 A 584 GLY ALA ALA ALA ASP LYS GLY ASP PRO VAL ASN ASP GLY SEQRES 25 A 584 PRO ALA TYR ILE ALA LEU MET ARG GLU LEU ARG VAL MET SEQRES 26 A 584 LEU ASP GLU LEU GLU ALA GLU THR GLY ARG THR TYR GLU SEQRES 27 A 584 LEU THR SER ALA ILE GLY VAL GLY TYR ASP LYS ILE GLU SEQRES 28 A 584 ASP VAL ASP TYR ALA ASP ALA VAL GLN TYR MET ASP TYR SEQRES 29 A 584 ILE PHE ALA MET THR TYR ASP PHE TYR GLY GLY TRP ASN SEQRES 30 A 584 ASN VAL PRO GLY HIS GLN THR ALA LEU TYR CYS GLY SER SEQRES 31 A 584 PHE MET ARG PRO GLY GLN CYS ASP GLY GLY GLY VAL ASP SEQRES 32 A 584 GLU ASN GLY GLU PRO TYR LYS GLY PRO ALA TYR THR ALA SEQRES 33 A 584 ASP ASN GLY ILE GLN LEU LEU LEU ALA GLN GLY VAL PRO SEQRES 34 A 584 ALA ASN LYS LEU VAL LEU GLY THR ALA MET TYR GLY ARG SEQRES 35 A 584 GLY TRP GLU GLY VAL THR PRO ASP THR LEU THR ASP PRO SEQRES 36 A 584 ASN ASP PRO MET THR GLY THR ALA THR GLY LYS LEU LYS SEQRES 37 A 584 GLY SER THR ALA GLN GLY VAL TRP GLU ASP GLY VAL ILE SEQRES 38 A 584 ASP TYR LYS GLY ILE LYS SER PHE MET LEU GLY ALA ASN SEQRES 39 A 584 ASN THR GLY ILE ASN GLY PHE GLU TYR GLY TYR ASP ALA SEQRES 40 A 584 GLN ALA GLU ALA PRO TRP VAL TRP ASN ARG SER THR GLY SEQRES 41 A 584 GLU LEU ILE THR PHE ASP ASP HIS ARG SER VAL LEU ALA SEQRES 42 A 584 LYS GLY ASN TYR ALA LYS SER LEU GLY LEU ALA GLY LEU SEQRES 43 A 584 PHE SER TRP GLU ILE ASP ALA ASP ASN GLY ASP ILE LEU SEQRES 44 A 584 ASN ALA MET HIS GLU GLY MET ALA GLY GLY VAL VAL THR SEQRES 45 A 584 PRO PRO ASN ARG ARG SER HIS HIS HIS HIS HIS HIS HET DM5 A 606 36 HET GOL A3500 12 HET GOL A3501 6 HET GOL A3502 6 HETNAM DM5 IDARUBICIN HETNAM GOL GLYCEROL HETSYN DM5 4-DEMETHOXY-DAUNORUBICIN HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 DM5 C26 H27 N O9 FORMUL 3 GOL 3(C3 H8 O3) FORMUL 6 HOH *826(H2 O) HELIX 1 1 MET A 30 ASN A 35 5 6 HELIX 2 2 GLY A 50 MET A 54 1 5 HELIX 3 3 TRP A 168 TYR A 171 5 4 HELIX 4 4 THR A 176 MET A 180 5 5 HELIX 5 5 PRO A 181 LEU A 185 5 5 HELIX 6 6 ASN A 199 GLY A 206 5 8 HELIX 7 7 ASN A 208 ARG A 218 1 11 HELIX 8 8 ASP A 229 GLN A 235 1 7 HELIX 9 9 PHE A 238 GLY A 242 5 5 HELIX 10 10 LYS A 250 ASN A 263 1 14 HELIX 11 11 SER A 278 VAL A 285 5 8 HELIX 12 12 ASP A 286 TRP A 304 1 19 HELIX 13 13 ASN A 331 GLY A 355 1 25 HELIX 14 14 GLY A 367 GLU A 372 1 6 HELIX 15 15 ASP A 375 VAL A 380 1 6 HELIX 16 16 GLN A 381 MET A 383 5 3 HELIX 17 17 THR A 436 GLN A 447 1 12 HELIX 18 18 PRO A 450 ASN A 452 5 3 HELIX 19 19 THR A 469 LEU A 473 5 5 HELIX 20 20 ASP A 478 GLY A 482 5 5 HELIX 21 21 SER A 491 GLY A 495 5 5 HELIX 22 22 TYR A 504 MET A 511 1 8 HELIX 23 23 ASP A 548 GLY A 563 1 16 HELIX 24 24 GLU A 571 ASP A 575 5 5 HELIX 25 25 GLY A 577 MET A 587 1 11 SHEET 1 A 3 SER A 27 ASP A 29 0 SHEET 2 A 3 ALA A 61 ASN A 68 -1 O LYS A 66 N ASP A 29 SHEET 3 A 3 GLN A 96 TYR A 103 -1 O PHE A 101 N ILE A 63 SHEET 1 B 5 GLN A 37 SER A 39 0 SHEET 2 B 5 VAL A 127 ALA A 132 1 O THR A 130 N PHE A 38 SHEET 3 B 5 GLY A 107 ASP A 117 -1 N MET A 111 O VAL A 127 SHEET 4 B 5 THR A 77 PHE A 82 -1 N ASN A 79 O GLU A 114 SHEET 5 B 5 VAL A 85 ALA A 91 -1 O VAL A 87 N VAL A 80 SHEET 1 C 4 GLN A 37 SER A 39 0 SHEET 2 C 4 VAL A 127 ALA A 132 1 O THR A 130 N PHE A 38 SHEET 3 C 4 GLY A 107 ASP A 117 -1 N MET A 111 O VAL A 127 SHEET 4 C 4 GLY A 120 LYS A 123 -1 O SER A 122 N ALA A 115 SHEET 1 D 2 ILE A 41 LEU A 43 0 SHEET 2 D 2 VAL A 55 TYR A 57 -1 O LYS A 56 N GLU A 42 SHEET 1 E 9 VAL A 160 VAL A 166 0 SHEET 2 E 9 HIS A 187 ILE A 193 1 O LEU A 189 N THR A 163 SHEET 3 E 9 LYS A 267 GLY A 273 1 O SER A 271 N TYR A 190 SHEET 4 E 9 GLY A 309 ASP A 313 1 O ASP A 311 N ILE A 272 SHEET 5 E 9 GLU A 359 GLY A 365 1 O THR A 361 N VAL A 310 SHEET 6 E 9 TYR A 385 MET A 389 1 O MET A 389 N ILE A 364 SHEET 7 E 9 LEU A 454 ALA A 459 1 O VAL A 455 N ILE A 386 SHEET 8 E 9 GLY A 566 TRP A 570 1 O PHE A 568 N THR A 458 SHEET 9 E 9 VAL A 160 VAL A 166 1 N GLY A 162 O LEU A 567 SHEET 1 F 3 GLY A 486 LYS A 487 0 SHEET 2 F 3 TYR A 461 GLU A 466 -1 N GLU A 466 O GLY A 486 SHEET 3 F 3 VAL A 501 ASP A 503 -1 O ILE A 502 N GLY A 462 SHEET 1 G 5 GLY A 486 LYS A 487 0 SHEET 2 G 5 TYR A 461 GLU A 466 -1 N GLU A 466 O GLY A 486 SHEET 3 G 5 GLU A 542 THR A 545 -1 O THR A 545 N ARG A 463 SHEET 4 G 5 ALA A 532 ASN A 537 -1 N ASN A 537 O GLU A 542 SHEET 5 G 5 PHE A 522 ASP A 527 -1 N ASP A 527 O ALA A 532 SSBOND 1 CYS A 116 CYS A 121 1555 1555 2.18 SSBOND 2 CYS A 196 CYS A 217 1555 1555 2.09 SSBOND 3 CYS A 409 CYS A 418 1555 1555 2.13 CISPEP 1 GLY A 191 PHE A 192 0 -7.69 CISPEP 2 GLY A 191 PHE A 192 0 -8.05 CISPEP 3 GLU A 315 PHE A 316 0 5.67 CISPEP 4 TRP A 570 GLU A 571 0 -15.35 CISPEP 5 TRP A 570 GLU A 571 0 -1.91 SITE 1 AC1 16 TRP A 275 GLY A 320 GLY A 321 LYS A 370 SITE 2 AC1 16 ASP A 392 PHE A 393 TRP A 397 TYR A 435 SITE 3 AC1 16 HOH A 805 HOH A 813 HOH A1009 HOH A1090 SITE 4 AC1 16 HOH A1097 HOH A1229 HOH A1290 GOL A3500 SITE 1 AC2 12 PHE A 316 GLY A 365 VAL A 366 GLY A 367 SITE 2 AC2 12 LYS A 370 MET A 389 TYR A 391 ASP A 392 SITE 3 AC2 12 TYR A 435 DM5 A 606 HOH A 805 HOH A 813 SITE 1 AC3 10 GLU A 114 CYS A 121 SER A 122 LYS A 123 SITE 2 AC3 10 GLY A 206 GLY A 207 ASN A 211 HOH A 868 SITE 3 AC3 10 HOH A 997 HOH A1147 SITE 1 AC4 9 LYS A 151 HIS A 549 ASP A 578 ASN A 581 SITE 2 AC4 9 ALA A 582 GLU A 585 HOH A1215 HOH A1266 SITE 3 AC4 9 HOH A1300 CRYST1 65.010 50.890 93.400 90.00 99.51 90.00 P 1 21 1 2 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 0.015382 0.000000 0.002576 0.00000 SCALE2 0.000000 0.019650 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010856 0.00000