HEADER HYDROLASE 06-MAR-17 5NCX OBSLTE 22-NOV-23 5NCX 8R06 TITLE CRYSTAL STRUCTURE OF THERMOANAEROBACTERIUM XYLOLYTICUM GH116 BETA- TITLE 2 GLUCOSIDASE WITH AN COVALENT INHIBITOR COMPND MOL_ID: 1; COMPND 2 MOLECULE: GLUCOSYLCERAMIDASE; COMPND 3 CHAIN: A; COMPND 4 EC: 3.2.1.45; COMPND 5 ENGINEERED: YES; COMPND 6 OTHER_DETAILS: RESIDUES 1-18, 789-799 ARE NOT VISIBLE IN THE COMPND 7 STRUCTURE. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: THERMOANAEROBACTERIUM XYLANOLYTICUM (STRAIN SOURCE 3 ATCC 49914 / DSM 7097 / LX-11); SOURCE 4 ORGANISM_TAXID: 858215; SOURCE 5 GENE: THEXY_2211; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS GH116, GLUCOCEREBROSIDASE, BETA-GLUCOSIDASE, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR G.J.DAVIES,I.Z.BREEN REVDAT 6 14-FEB-24 5NCX 1 REMARK REVDAT 5 22-NOV-23 5NCX 1 OBSLTE REVDAT 4 28-FEB-18 5NCX 1 SOURCE REVDAT 3 24-JAN-18 5NCX 1 SOURCE REVDAT 2 18-OCT-17 5NCX 1 JRNL REVDAT 1 04-OCT-17 5NCX 0 JRNL AUTH D.LAHAV,B.LIU,R.J.B.H.N.VAN DEN BERG, JRNL AUTH 2 A.M.C.H.VAN DEN NIEUWENDIJK,T.WENNEKES,A.T.GHISAIDOOBE, JRNL AUTH 3 I.BREEN,M.J.FERRAZ,C.L.KUO,L.WU,P.P.GEURINK,H.OVAA, JRNL AUTH 4 G.A.VAN DER MAREL,M.VAN DER STELT,R.G.BOOT,G.J.DAVIES, JRNL AUTH 5 J.M.F.G.AERTS,H.S.OVERKLEEFT JRNL TITL A FLUORESCENCE POLARIZATION ACTIVITY-BASED PROTEIN PROFILING JRNL TITL 2 ASSAY IN THE DISCOVERY OF POTENT, SELECTIVE INHIBITORS FOR JRNL TITL 3 HUMAN NONLYSOSOMAL GLUCOSYLCERAMIDASE. JRNL REF J. AM. CHEM. SOC. V. 139 14192 2017 JRNL REFN ESSN 1520-5126 JRNL PMID 28937220 JRNL DOI 10.1021/JACS.7B07352 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0158 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 60.73 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 83283 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) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.154 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 : 4371 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6065 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.85 REMARK 3 BIN R VALUE (WORKING SET) : 0.2680 REMARK 3 BIN FREE R VALUE SET COUNT : 306 REMARK 3 BIN FREE R VALUE : 0.2920 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 6213 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 26 REMARK 3 SOLVENT ATOMS : 371 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.07 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.48000 REMARK 3 B22 (A**2) : -0.65000 REMARK 3 B33 (A**2) : 0.17000 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): 0.091 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.090 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.064 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.011 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 6430 ; 0.018 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): 5665 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 8721 ; 1.873 ; 1.934 REMARK 3 BOND ANGLES OTHERS (DEGREES): 13206 ; 1.069 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 772 ; 7.064 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 309 ;37.182 ;25.243 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1064 ;13.367 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;22.664 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 885 ; 0.121 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 7179 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1361 ; 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): 3085 ; 1.780 ; 1.836 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 3084 ; 1.779 ; 1.836 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3855 ; 2.582 ; 2.751 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3856 ; 2.581 ; 2.751 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3345 ; 2.819 ; 2.100 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 3345 ; 2.818 ; 2.100 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4866 ; 4.247 ; 3.020 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 7563 ; 5.181 ;21.281 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 7563 ; 5.180 ;21.279 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 : 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. SUGAR RING OF LIGAND MODELLED AT AN OCCUPANCY OF 1.0. REMARK 3 INSUFFICIENT DENSITY TO MODEL CO(CH2)3CH3 GROUP ON N ATOM OF REMARK 3 LIGAND. RESIDUES 33-36, 430-431, 802-803 ARE MODELLED AT AN REMARK 3 OCCUPANCY OF 0.5. REMARK 4 REMARK 4 5NCX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-MAR-17. REMARK 100 THE DEPOSITION ID IS D_1200003891. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-SEP-16 REMARK 200 TEMPERATURE (KELVIN) : 120 REMARK 200 PH : 5.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9763 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 87708 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 60.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 5.700 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 5.60 REMARK 200 R MERGE FOR SHELL (I) : 0.90100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.700 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: 5BVU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.13 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.16 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 20% PEG 3350, REMARK 280 0.1M BISTRIS, PH 5.7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE REMARK 280 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 2 21 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,-Z+1/2 REMARK 290 4555 -X+1/2,-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 -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 26.81050 REMARK 290 SMTRY2 3 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 88.74000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 26.81050 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 88.74000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 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 ALA A 16 REMARK 465 MET A 17 REMARK 465 ALA A 18 REMARK 465 LEU A 19 REMARK 465 THR A 20 REMARK 465 GLY A 21 REMARK 465 CYS A 22 REMARK 465 SER A 23 REMARK 465 GLU A 24 REMARK 465 LYS A 25 REMARK 465 ILE A 26 REMARK 465 ASN A 27 REMARK 465 ILE A 28 REMARK 465 ASN A 29 REMARK 465 GLU A 30 REMARK 465 ASP A 31 REMARK 465 LYS A 32 REMARK 465 ASN A 804 REMARK 465 GLU A 805 REMARK 465 VAL A 806 REMARK 465 LEU A 807 REMARK 465 GLU A 808 REMARK 465 HIS A 809 REMARK 465 HIS A 810 REMARK 465 HIS A 811 REMARK 465 HIS A 812 REMARK 465 HIS A 813 REMARK 465 HIS A 814 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 SER A 34 OG REMARK 470 HIS A 35 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 36 CG CD CE NZ REMARK 470 LYS A 61 CG CD CE NZ REMARK 470 LYS A 121 CG CD CE NZ REMARK 470 ASN A 135 CG OD1 ND2 REMARK 470 LYS A 240 CD CE NZ REMARK 470 LYS A 429 CG CD CE NZ REMARK 470 ASP A 430 CG OD1 OD2 REMARK 470 LYS A 431 CG CD CE NZ REMARK 470 LYS A 489 CD CE NZ REMARK 470 ASN A 802 CG OD1 ND2 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 1215 O HOH A 1348 1.88 REMARK 500 OE2 GLU A 333 O HOH A 1001 1.95 REMARK 500 O HOH A 1082 O HOH A 1349 1.96 REMARK 500 O HOH A 1005 O HOH A 1323 1.97 REMARK 500 NZ LYS A 744 O HOH A 1002 2.13 REMARK 500 O HOH A 1017 O HOH A 1286 2.18 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 1108 O HOH A 1341 3565 1.93 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 GLU A 441 CD GLU A 441 OE2 0.273 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 PHE A 78 CB - CG - CD2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ASP A 387 CB - CG - OD1 ANGL. DEV. = 6.0 DEGREES REMARK 500 ASP A 416 CB - CG - OD1 ANGL. DEV. = 5.8 DEGREES REMARK 500 ARG A 432 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 ARG A 432 NE - CZ - NH2 ANGL. DEV. = -4.6 DEGREES REMARK 500 ASP A 667 CB - CG - OD2 ANGL. DEV. = -6.5 DEGREES REMARK 500 ASP A 722 CB - CG - OD1 ANGL. DEV. = 6.8 DEGREES REMARK 500 ARG A 792 NE - CZ - NH1 ANGL. DEV. = 3.2 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 68 170.77 82.27 REMARK 500 ASN A 135 -99.30 -85.28 REMARK 500 LYS A 186 -80.30 -111.55 REMARK 500 LYS A 240 69.70 -114.14 REMARK 500 THR A 286 49.15 -95.87 REMARK 500 ASN A 299 11.87 -145.97 REMARK 500 ASP A 307 104.85 -166.73 REMARK 500 LYS A 312 -71.37 -109.89 REMARK 500 LYS A 429 -74.97 -80.23 REMARK 500 CYS A 442 -177.57 -177.77 REMARK 500 ASN A 493 11.05 -142.37 REMARK 500 ALA A 514 -117.17 -131.44 REMARK 500 TRP A 517 -19.15 73.71 REMARK 500 ASP A 589 49.54 -100.92 REMARK 500 PHE A 699 -75.22 -101.53 REMARK 500 VAL A 701 -65.96 -90.62 REMARK 500 ARG A 774 42.46 -160.52 REMARK 500 ALA A 787 77.62 69.66 REMARK 500 MET A 789 67.95 61.28 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 ASN A 135 GLY A 136 -130.04 REMARK 500 GLY A 136 TYR A 137 -148.95 REMARK 500 ASP A 243 SER A 244 148.14 REMARK 500 REMARK 500 REMARK: NULL 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 K35 A 901 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 902 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 575 OD1 REMARK 620 2 ASP A 577 OD1 77.9 REMARK 620 3 ASP A 579 OD1 84.5 81.1 REMARK 620 4 ILE A 581 O 82.7 160.3 94.0 REMARK 620 5 ASP A 583 OD1 92.3 96.0 176.1 87.9 REMARK 620 6 HOH A1011 O 166.2 115.4 94.0 83.8 89.6 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 K35 A 901 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CA A 902 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 903 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 904 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 905 DBREF 5NCX A 19 806 UNP F6BL85 F6BL85_THEXL 19 806 SEQADV 5NCX ALA A 16 UNP F6BL85 EXPRESSION TAG SEQADV 5NCX MET A 17 UNP F6BL85 EXPRESSION TAG SEQADV 5NCX ALA A 18 UNP F6BL85 EXPRESSION TAG SEQADV 5NCX LEU A 807 UNP F6BL85 EXPRESSION TAG SEQADV 5NCX GLU A 808 UNP F6BL85 EXPRESSION TAG SEQADV 5NCX HIS A 809 UNP F6BL85 EXPRESSION TAG SEQADV 5NCX HIS A 810 UNP F6BL85 EXPRESSION TAG SEQADV 5NCX HIS A 811 UNP F6BL85 EXPRESSION TAG SEQADV 5NCX HIS A 812 UNP F6BL85 EXPRESSION TAG SEQADV 5NCX HIS A 813 UNP F6BL85 EXPRESSION TAG SEQADV 5NCX HIS A 814 UNP F6BL85 EXPRESSION TAG SEQRES 1 A 799 ALA MET ALA LEU THR GLY CYS SER GLU LYS ILE ASN ILE SEQRES 2 A 799 ASN GLU ASP LYS ILE SER HIS LYS ILE ASP ILE PRO ASP SEQRES 3 A 799 SER ALA TRP THR ILE GLY ILE GLY GLU LYS PHE LYS ASN SEQRES 4 A 799 ALA GLY HIS PRO ASN VAL LYS TYR PRO MET ILE ASP ASP SEQRES 5 A 799 SER TYR VAL GLN GLY ALA PRO LEU GLY GLY PHE GLY ALA SEQRES 6 A 799 GLY THR ILE GLY ARG THR TYR ASN GLY GLY PHE SER ARG SEQRES 7 A 799 TRP HIS LEU GLU ILE GLY LYS ASN LYS TYR THR THR VAL SEQRES 8 A 799 TYR ALA ASN GLN PHE SER VAL PHE GLN LYS VAL GLU GLY SEQRES 9 A 799 ASN LYS ASP GLY VAL ALA GLN VAL LEU TYR ALA GLY GLU SEQRES 10 A 799 PRO GLU ASN GLY TYR LEU SER SER TRP LYS TRP ASP TYR SEQRES 11 A 799 PRO LYS GLU SER GLY MET TYR TYR ALA LEU TYR PRO ASN SEQRES 12 A 799 SER TRP TYR THR TYR THR ASN LYS ASP LEU PRO VAL GLN SEQRES 13 A 799 LEU ALA VAL LYS GLN PHE SER PRO ILE ILE PRO TYR ASN SEQRES 14 A 799 TYR LYS GLU THR SER TYR PRO VAL ALA VAL PHE LYS TRP SEQRES 15 A 799 THR ALA TYR ASN PRO THR ASN LYS ASN VAL ASP VAL SER SEQRES 16 A 799 ILE MET PHE THR TRP GLN ASN MET ILE GLY PHE PHE GLY SEQRES 17 A 799 LYS GLN VAL ASN VAL ASN SER GLY ASN PHE ASN LYS ILE SEQRES 18 A 799 ILE LYS ASP LYS SER LYS ASP SER GLU ILE VAL ALA ALA SEQRES 19 A 799 VAL MET GLY ASN ILE SER ASN ASP ASN GLU GLU TRP ASN SEQRES 20 A 799 GLY GLU TYR SER ILE GLY VAL LYS LYS VAL PRO GLY VAL SEQRES 21 A 799 ASP ILE SER TYR LYS ALA LYS PHE VAL THR THR GLY ASP SEQRES 22 A 799 GLY SER ASP LEU TRP HIS GLU PHE SER LYS ASN GLY ILE SEQRES 23 A 799 LEU ASP ASN LYS ASP ASP GLU THR PRO THR LYS GLN ASP SEQRES 24 A 799 GLY ILE GLY SER ALA ILE ALA VAL ASN PHE LYS LEU GLN SEQRES 25 A 799 PRO GLY GLN THR ILE GLU VAL PRO PHE ALA LEU SER TRP SEQRES 26 A 799 ASP LEU PRO ILE MET LYS PHE GLY GLY GLY ASP LYS TRP SEQRES 27 A 799 TYR LYS MET TYR THR LYS TYR PHE GLY LYS ASN GLY LYS SEQRES 28 A 799 ASN SER PHE ALA ILE LEU LYS GLU ALA LEU ASN ASN TYR SEQRES 29 A 799 GLN LYS TRP GLU LYS MET ILE ASP ASP TRP GLN LYS PRO SEQRES 30 A 799 ILE LEU SER ASN LYS SER LYS PRO ASP TRP TYR LYS THR SEQRES 31 A 799 ALA LEU PHE ASN GLU LEU TYR TYR LEU ALA ASP GLY GLY SEQRES 32 A 799 THR ALA TRP GLU ASN GLY LYS VAL GLY GLU LYS ASP LYS SEQRES 33 A 799 ARG THR ASN ASN MET PHE GLY LEU LEU GLU CYS PHE ASP SEQRES 34 A 799 TYR ASN TYR TYR GLU THR LEU ASP VAL ARG PHE TYR GLY SEQRES 35 A 799 SER PHE PRO LEU VAL MET LEU TRP PRO ASP ILE GLU LYS SEQRES 36 A 799 GLN VAL MET ARG GLN PHE ALA ASP THR ILE ASN VAL GLN SEQRES 37 A 799 ASP SER SER GLU PHE LYS VAL GLY SER ASN GLY ALA MET SEQRES 38 A 799 ALA VAL LYS LYS VAL GLN GLY MET ILE PRO HIS ASP LEU SEQRES 39 A 799 GLY SER SER TYR ALA LEU PRO TRP ILE LYS ILE ASN ALA SEQRES 40 A 799 TYR ASP TRP GLN ASN PRO ASN ILE TRP LYS ASP LEU ASN SEQRES 41 A 799 SER LYS TYR VAL LEU LEU VAL TYR ARG ASP TYR VAL LEU SEQRES 42 A 799 THR GLY LYS THR ASP LYS GLU PHE LEU LYS TYR THR TRP SEQRES 43 A 799 LYS SER VAL LYS THR ALA LEU ASP LYS LEU LYS GLU MET SEQRES 44 A 799 ASP LYS ASP ASN ASP GLY ILE PRO ASP ASN GLU GLY ILE SEQRES 45 A 799 PRO ASP GLN THR TYR ASP THR TRP SER MET LYS GLY THR SEQRES 46 A 799 SER ALA TYR CYS GLY SER LEU TRP LEU ALA ALA LEU LYS SEQRES 47 A 799 ALA ALA GLN GLU ILE GLY LYS VAL LEU LYS ASP ASN GLU SEQRES 48 A 799 ALA TYR ILE LYS TYR ASN GLU TRP TYR LYS ILE ALA GLN SEQRES 49 A 799 GLN ASN PHE GLU LYS GLU LEU TRP ASN GLY GLU TYR TYR SEQRES 50 A 799 ASN PHE ASP THR GLU SER ASP HIS LYS ASP SER ILE MET SEQRES 51 A 799 ALA ASP GLN LEU ALA GLY GLN TRP TYR ALA ASP ILE LEU SEQRES 52 A 799 ARG LEU GLY ASP ILE LEU PRO LYS ASP HIS VAL GLN LYS SEQRES 53 A 799 ALA LEU LYS LYS ILE TYR GLU PHE ASN VAL MET LYS PHE SEQRES 54 A 799 GLU ASN GLY LYS MET GLY ALA VAL ASN GLY MET ARG PRO SEQRES 55 A 799 ASP GLY ILE VAL ASP GLU SER ASP ILE GLN ALA GLN GLU SEQRES 56 A 799 VAL TRP THR GLY VAL THR TYR ALA LEU ALA SER PHE MET SEQRES 57 A 799 LYS TYR ARG GLY MET THR GLU GLU ALA TYR ASN THR ALA SEQRES 58 A 799 TYR GLY VAL TYR LYS MET THR TYR ASP LYS SER GLY LYS SEQRES 59 A 799 GLY TYR TRP PHE ARG THR PRO GLU ALA TRP THR LYS ASP SEQRES 60 A 799 GLY ASN TYR ARG ALA SER MET TYR MET ARG PRO LEU SER SEQRES 61 A 799 ILE TRP SER MET GLU VAL ASN TYR ASN GLU VAL LEU GLU SEQRES 62 A 799 HIS HIS HIS HIS HIS HIS HET K35 A 901 12 HET CA A 902 1 HET GOL A 903 6 HET GOL A 904 6 HET CL A 905 1 HETNAM K35 ~{N}-[(1~{R},2~{R},3~{R},4~{S},5~{S},6~{S})-2- HETNAM 2 K35 (HYDROXYMETHYL)-3,4,5,6-TETRAKIS(OXIDANYL) HETNAM 3 K35 CYCLOHEXYL]PENTANAMIDE HETNAM CA CALCIUM ION HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 K35 C12 H23 N O6 FORMUL 3 CA CA 2+ FORMUL 4 GOL 2(C3 H8 O3) FORMUL 6 CL CL 1- FORMUL 7 HOH *371(H2 O) HELIX 1 AA1 LYS A 186 TYR A 190 5 5 HELIX 2 AA2 GLY A 289 GLY A 300 1 12 HELIX 3 AA3 TYR A 357 GLY A 362 1 6 HELIX 4 AA4 ASN A 367 SER A 395 1 29 HELIX 5 AA5 PRO A 400 LEU A 411 1 12 HELIX 6 AA6 LEU A 411 GLY A 417 1 7 HELIX 7 AA7 THR A 450 SER A 458 1 9 HELIX 8 AA8 SER A 458 TRP A 465 1 8 HELIX 9 AA9 TRP A 465 ILE A 480 1 16 HELIX 10 AB1 ASN A 527 TRP A 531 5 5 HELIX 11 AB2 ASP A 533 THR A 549 1 17 HELIX 12 AB3 ASP A 553 GLU A 573 1 21 HELIX 13 AB4 SER A 601 LYS A 623 1 23 HELIX 14 AB5 ASP A 624 TRP A 647 1 24 HELIX 15 AB6 LEU A 669 LEU A 678 1 10 HELIX 16 AB7 PRO A 685 PHE A 699 1 15 HELIX 17 AB8 PHE A 704 LYS A 708 5 5 HELIX 18 AB9 ASP A 725 GLU A 730 5 6 HELIX 19 AC1 THR A 733 ARG A 746 1 14 HELIX 20 AC2 MET A 748 ASP A 765 1 18 HELIX 21 AC3 MET A 791 VAL A 801 5 11 SHEET 1 AA1 9 TRP A 44 GLY A 47 0 SHEET 2 AA1 9 GLY A 150 LEU A 155 -1 O TYR A 152 N ILE A 46 SHEET 3 AA1 9 ASN A 158 TYR A 163 -1 O TRP A 160 N TYR A 153 SHEET 4 AA1 9 GLN A 171 PHE A 177 -1 O GLN A 176 N SER A 159 SHEET 5 AA1 9 VAL A 192 TYR A 200 -1 O LYS A 196 N LYS A 175 SHEET 6 AA1 9 THR A 331 ASP A 341 -1 O ILE A 332 N ALA A 199 SHEET 7 AA1 9 GLU A 264 LYS A 270 -1 N GLU A 264 O ASP A 341 SHEET 8 AA1 9 ILE A 246 ASN A 253 -1 N MET A 251 O TYR A 265 SHEET 9 AA1 9 ASN A 232 ASP A 239 -1 N ASP A 239 O ILE A 246 SHEET 1 AA2 4 PRO A 74 LEU A 75 0 SHEET 2 AA2 4 THR A 82 ARG A 85 -1 O ILE A 83 N LEU A 75 SHEET 3 AA2 4 PHE A 91 HIS A 95 -1 O ARG A 93 N GLY A 84 SHEET 4 AA2 4 LYS A 102 TYR A 103 -1 O LYS A 102 N TRP A 94 SHEET 1 AA3 5 VAL A 124 VAL A 127 0 SHEET 2 AA3 5 GLN A 110 VAL A 117 -1 N VAL A 113 O GLN A 126 SHEET 3 AA3 5 VAL A 207 GLN A 216 -1 O THR A 214 N GLN A 110 SHEET 4 AA3 5 ILE A 316 LEU A 326 -1 O ILE A 320 N PHE A 213 SHEET 5 AA3 5 VAL A 275 VAL A 284 -1 N SER A 278 O ALA A 321 SHEET 1 AA4 4 ILE A 344 LYS A 346 0 SHEET 2 AA4 4 LYS A 352 LYS A 355 -1 O TRP A 353 N MET A 345 SHEET 3 AA4 4 ALA A 420 LYS A 425 -1 O GLY A 424 N TYR A 354 SHEET 4 AA4 4 PHE A 437 GLY A 438 -1 O GLY A 438 N ALA A 420 SHEET 1 AA5 2 ASP A 484 LYS A 489 0 SHEET 2 AA5 2 MET A 496 LYS A 500 -1 O LYS A 500 N ASP A 484 SHEET 1 AA6 2 ASN A 584 ILE A 587 0 SHEET 2 AA6 2 MET A 597 GLY A 599 -1 O GLY A 599 N ASN A 584 SHEET 1 AA7 2 ILE A 664 MET A 665 0 SHEET 2 AA7 2 GLY A 714 MET A 715 -1 O MET A 715 N ILE A 664 SHEET 1 AA8 3 VAL A 731 TRP A 732 0 SHEET 2 AA8 3 ALA A 778 TRP A 779 -1 O TRP A 779 N VAL A 731 SHEET 3 AA8 3 TYR A 785 ARG A 786 -1 O ARG A 786 N ALA A 778 LINK OE2 GLU A 441 C7 K35 A 901 1555 1555 1.53 LINK OD1 ASP A 575 CA CA A 902 1555 1555 2.27 LINK OD1 ASP A 577 CA CA A 902 1555 1555 2.35 LINK OD1 ASP A 579 CA CA A 902 1555 1555 2.23 LINK O ILE A 581 CA CA A 902 1555 1555 2.23 LINK OD1 ASP A 583 CA CA A 902 1555 1555 2.20 LINK CA CA A 902 O HOH A1011 1555 1555 2.33 CISPEP 1 TYR A 156 PRO A 157 0 14.60 SITE 1 AC1 11 GLU A 441 TYR A 445 ASP A 452 HIS A 507 SITE 2 AC1 11 TYR A 523 THR A 591 ASP A 593 GLU A 777 SITE 3 AC1 11 ARG A 786 TYR A 790 ARG A 792 SITE 1 AC2 6 ASP A 575 ASP A 577 ASP A 579 ILE A 581 SITE 2 AC2 6 ASP A 583 HOH A1011 SITE 1 AC3 4 GLY A 362 LYS A 363 ASN A 364 HOH A1023 SITE 1 AC4 4 ARG A 432 THR A 433 ASN A 434 HOH A1162 SITE 1 AC5 1 LYS A 708 CRYST1 53.621 83.295 177.480 90.00 90.00 90.00 P 21 2 21 4 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 0.018649 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012006 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005634 0.00000