HEADER CARBOHYDRATE 23-SEP-21 7PSJ TITLE CRYSTAL STRUCTURE OF BETA-GLUCURONIDASE FROM ACIDOBACTERIUM CAPSULATUM TITLE 2 IN COMPLEX WITH COVALENT INHIBITOR VL166 COMPND MOL_ID: 1; COMPND 2 MOLECULE: BETA-GLUCURONIDASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ACIDOBACTERIUM CAPSULATUM (STRAIN ATCC 51196 / SOURCE 3 DSM 11244 / JCM 7670 / NBRC 15755 / NCIMB 13165 / 161); SOURCE 4 ORGANISM_TAXID: 240015; SOURCE 5 STRAIN: ATCC 51196 / DSM 11244 / JCM 7670 / NBRC 15755 / NCIMB 13165 SOURCE 6 / 161; SOURCE 7 GENE: ACP_2665; SOURCE 8 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 9 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLYCOSIDE HYDROLASE, CARBOHYDRATE, GLUCURONIDASE, GH79, HEPARAN KEYWDS 2 SULFATE EXPDTA X-RAY DIFFRACTION AUTHOR Z.ARMSTRONG,L.WU,G.J.DAVIES REVDAT 2 31-JAN-24 7PSJ 1 REMARK REVDAT 1 03-AUG-22 7PSJ 0 JRNL AUTH C.DE BOER,Z.ARMSTRONG,V.A.J.LIT,U.BARASH,G.RUIJGROK, JRNL AUTH 2 I.BOYANGO,M.M.WEITZENBERG,S.P.SCHRODER,A.J.C.SARRIS, JRNL AUTH 3 N.J.MEEUWENOORD,P.BULE,Y.KAYAL,N.ILAN,J.D.C.CODEE, JRNL AUTH 4 I.VLODAVSKY,H.S.OVERKLEEFT,G.J.DAVIES,L.WU JRNL TITL MECHANISM-BASED HEPARANASE INHIBITORS REDUCE CANCER JRNL TITL 2 METASTASIS IN VIVO. JRNL REF PROC.NATL.ACAD.SCI.USA V. 119 67119 2022 JRNL REFN ESSN 1091-6490 JRNL PMID 35881786 JRNL DOI 10.1073/PNAS.2203167119 REMARK 2 REMARK 2 RESOLUTION. 1.55 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 1.55 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 75.11 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 71856 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : FREE R-VALUE REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.195 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3593 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) : 1.55 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.59 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5029 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.79 REMARK 3 BIN R VALUE (WORKING SET) : 0.3320 REMARK 3 BIN FREE R VALUE SET COUNT : 270 REMARK 3 BIN FREE R VALUE : 0.3270 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3312 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 360 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.82 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.53500 REMARK 3 B22 (A**2) : 3.60500 REMARK 3 B33 (A**2) : -2.17400 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.68400 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.081 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.082 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.952 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3445 ; 0.011 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3092 ; 0.036 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4691 ; 1.643 ; 1.661 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7162 ; 2.527 ; 1.582 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 435 ; 6.689 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 176 ;29.610 ;21.875 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 500 ;13.328 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;16.476 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 445 ; 0.200 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3942 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 765 ; 0.014 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 666 ; 0.206 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 56 ; 0.198 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1710 ; 0.174 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 285 ; 0.150 ; 0.200 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): 1749 ; 1.752 ; 2.135 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1748 ; 1.729 ; 2.135 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2181 ; 2.574 ; 3.186 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2182 ; 2.576 ; 3.187 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1696 ; 2.497 ; 2.413 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1697 ; 2.497 ; 2.413 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2510 ; 3.799 ; 3.517 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2511 ; 3.798 ; 3.517 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 BULK SOLVENT 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 THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 7PSJ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 28-SEP-21. REMARK 100 THE DEPOSITION ID IS D_1292118274. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JAN-20 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979499 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 71878 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.550 REMARK 200 RESOLUTION RANGE LOW (A) : 75.110 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 7.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.55 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.58 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5G0M REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.5 M AMSO4 1 M LISO4 0.1 M TRISODIUM REMARK 280 CITRATE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z+1/2 REMARK 290 4555 -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 32.68108 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 22.05850 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 67.75686 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 32.68108 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 22.05850 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 67.75686 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 TOTAL BURIED SURFACE AREA: 360 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17050 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 3.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B 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 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 644 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 821 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 465 ALA A 2 REMARK 465 PHE A 3 REMARK 465 ALA A 4 REMARK 465 ARG A 5 REMARK 465 GLY A 6 REMARK 465 GLY A 7 REMARK 465 LEU A 8 REMARK 465 ALA A 9 REMARK 465 GLN A 10 REMARK 465 THR A 11 REMARK 465 ALA A 12 REMARK 465 SER A 13 REMARK 465 GLN A 14 REMARK 465 ALA A 91 REMARK 465 LYS A 92 REMARK 465 PRO A 93 REMARK 465 THR A 94 REMARK 465 ALA A 95 REMARK 465 ALA A 96 REMARK 465 ASP A 97 REMARK 465 GLU A 98 REMARK 465 HIS A 99 REMARK 465 LEU A 100 REMARK 465 ALA A 101 REMARK 465 ALA A 102 REMARK 465 GLY A 103 REMARK 465 PRO A 104 REMARK 465 ASP A 105 REMARK 465 LYS A 106 REMARK 465 GLY A 107 REMARK 465 HIS A 108 REMARK 465 HIS A 109 REMARK 465 ALA A 110 REMARK 465 ALA A 111 REMARK 465 ALA A 112 REMARK 465 PRO A 248 REMARK 465 THR A 249 REMARK 465 HIS A 456 REMARK 465 SER A 457 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 OH TYR A 219 O HOH A 601 2.09 REMARK 500 OE1 GLU A 245 SG CYS A 291 2.12 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 287 CD GLU A 287 OE2 0.119 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 THR A 217 CA - CB - OG1 ANGL. DEV. = -15.5 DEGREES REMARK 500 MET A 253 N - CA - CB ANGL. DEV. = 11.8 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 17 -73.02 -71.50 REMARK 500 TYR A 54 -71.82 -81.48 REMARK 500 TRP A 223 -59.30 -121.11 REMARK 500 PRO A 251 6.52 -60.56 REMARK 500 VAL A 299 -66.83 -127.43 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 960 DISTANCE = 6.79 ANGSTROMS DBREF 7PSJ A 1 475 UNP C1F2K5 C1F2K5_ACIC5 1 475 SEQRES 1 A 475 MET ALA PHE ALA ARG GLY GLY LEU ALA GLN THR ALA SER SEQRES 2 A 475 GLN THR THR SER SER PRO VAL ARG VAL GLY LEU SER VAL SEQRES 3 A 475 ASP ALA SER ALA LEU GLY HIS THR ILE PRO PRO ASP TYR SEQRES 4 A 475 THR GLY LEU SER TYR GLU GLN ALA GLN MET ALA ASN PRO SEQRES 5 A 475 ASN TYR PHE SER GLY ALA ASN THR GLN LEU ALA GLY PHE SEQRES 6 A 475 LEU ARG THR LEU GLY ARG GLN GLY VAL LEU ARG ILE GLY SEQRES 7 A 475 GLY ASN THR SER GLU TYR THR PHE TRP ASN ARG HIS ALA SEQRES 8 A 475 LYS PRO THR ALA ALA ASP GLU HIS LEU ALA ALA GLY PRO SEQRES 9 A 475 ASP LYS GLY HIS HIS ALA ALA ALA ARG GLU VAL ILE THR SEQRES 10 A 475 PRO GLU ALA VAL ASN ASN LEU SER GLU PHE LEU ASP LYS SEQRES 11 A 475 THR GLY TRP LYS LEU ILE TYR GLY LEU ASN LEU GLY LYS SEQRES 12 A 475 GLY THR PRO GLU ASN ALA ALA ASP GLU ALA ALA TYR VAL SEQRES 13 A 475 MET GLU THR ILE GLY ALA ASP ARG LEU LEU ALA PHE GLN SEQRES 14 A 475 LEU GLY ASN GLU PRO ASP LEU PHE TYR ARG ASN GLY ILE SEQRES 15 A 475 ARG PRO ALA SER TYR ASP PHE ALA ALA TYR ALA GLY ASP SEQRES 16 A 475 TRP GLN ARG PHE PHE THR ALA ILE ARG LYS ARG VAL PRO SEQRES 17 A 475 ASN ALA PRO PHE ALA GLY PRO ASP THR ALA TYR ASN THR SEQRES 18 A 475 LYS TRP LEU VAL PRO PHE ALA ASP LYS PHE LYS HIS ASP SEQRES 19 A 475 VAL LYS PHE ILE SER SER HIS TYR TYR ALA GLU GLY PRO SEQRES 20 A 475 PRO THR ASP PRO SER MET THR ILE GLU ARG LEU MET LYS SEQRES 21 A 475 PRO ASN PRO ARG LEU LEU GLY GLU THR ALA GLY LEU LYS SEQRES 22 A 475 GLN VAL GLU ALA ASP THR GLY LEU PRO PHE ARG LEU THR SEQRES 23 A 475 GLU THR ASN SER CYS TYR GLN GLY GLY LYS GLN GLY VAL SEQRES 24 A 475 SER ASP THR PHE ALA ALA ALA LEU TRP ALA GLY ASP LEU SEQRES 25 A 475 MET TYR GLN GLN ALA ALA ALA GLY SER THR GLY ILE ASN SEQRES 26 A 475 PHE HIS GLY GLY GLY TYR GLY TRP TYR THR PRO VAL ALA SEQRES 27 A 475 GLY THR PRO GLU ASP GLY PHE ILE ALA ARG PRO GLU TYR SEQRES 28 A 475 TYR GLY MET LEU LEU PHE ALA GLN ALA GLY ALA GLY GLN SEQRES 29 A 475 LEU LEU GLY ALA LYS LEU THR ASP ASN SER ALA ALA PRO SEQRES 30 A 475 LEU LEU THR ALA TYR ALA LEU ARG GLY THR ASP GLY ARG SEQRES 31 A 475 THR ARG ILE ALA LEU PHE ASN LYS ASN LEU ASP ALA ASP SEQRES 32 A 475 VAL GLU VAL ALA ILE SER GLY VAL ALA SER PRO SER GLY SEQRES 33 A 475 THR VAL LEU ARG LEU GLU ALA PRO ARG ALA ASP ASP THR SEQRES 34 A 475 THR ASP VAL THR PHE GLY GLY ALA PRO VAL GLY ALA SER SEQRES 35 A 475 GLY SER TRP SER PRO LEU VAL GLN GLU TYR VAL PRO GLY SEQRES 36 A 475 HIS SER GLY GLN PHE VAL LEU HIS MET ARG LYS ALA SER SEQRES 37 A 475 GLY ALA LEU LEU GLU PHE ALA HET 8I4 B 1 13 HET NDG B 2 14 HETNAM 8I4 (2R,3S,5R,6R)-2,3,4,5,6-PENTAKIS(OXIDANYL)CYCLOHEXANE- HETNAM 2 8I4 1-CARBOXYLIC ACID HETNAM NDG 2-ACETAMIDO-2-DEOXY-ALPHA-D-GLUCOPYRANOSE HETSYN 8I4 (2R)-5-[(E)-2-(2,4-DINITROPHENYL)ETHENYL]-2-[(1R)-2- HETSYN 2 8I4 OXIDANYL-2-OXIDANYLIDENE-1-(2-THIOPHEN-2- HETSYN 3 8I4 YLETHANOYLAMINO)ETHYL]-3,6-DIHYDRO-2H-1,3-THIAZINE-4- HETSYN 4 8I4 CARBOXYLIC ACID HETSYN NDG N-ACETYL-ALPHA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY- HETSYN 2 NDG ALPHA-D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2- HETSYN 3 NDG ACETAMIDO-2-DEOXY-GLUCOSE; 2-(ACETYLAMINO)-2-DEOXY-A- HETSYN 4 NDG D-GLUCOPYRANOSE FORMUL 2 8I4 C7 H12 O7 FORMUL 2 NDG C8 H15 N O6 FORMUL 3 HOH *360(H2 O) HELIX 1 AA1 ALA A 47 ASN A 51 5 5 HELIX 2 AA2 ASN A 59 GLY A 70 1 12 HELIX 3 AA3 GLY A 79 GLU A 83 5 5 HELIX 4 AA4 THR A 117 GLY A 132 1 16 HELIX 5 AA5 THR A 145 ILE A 160 1 16 HELIX 6 AA6 GLU A 173 PHE A 177 5 5 HELIX 7 AA7 ASP A 188 VAL A 207 1 20 HELIX 8 AA8 TRP A 223 LYS A 232 1 10 HELIX 9 AA9 THR A 254 LYS A 260 1 7 HELIX 10 AB1 ASN A 262 GLY A 280 1 19 HELIX 11 AB2 THR A 302 ALA A 319 1 18 HELIX 12 AB3 ARG A 348 GLY A 361 1 14 HELIX 13 AB4 GLY A 440 SER A 444 5 5 SHEET 1 AA1 3 THR A 433 PHE A 434 0 SHEET 2 AA1 3 GLY A 416 GLU A 422 -1 N GLU A 422 O THR A 433 SHEET 3 AA1 3 GLU A 451 VAL A 453 -1 O VAL A 453 N GLY A 416 SHEET 1 AA2 9 THR A 433 PHE A 434 0 SHEET 2 AA2 9 GLY A 416 GLU A 422 -1 N GLU A 422 O THR A 433 SHEET 3 AA2 9 SER A 468 PHE A 474 -1 O GLY A 469 N LEU A 421 SHEET 4 AA2 9 THR A 391 ASN A 397 -1 N ILE A 393 O LEU A 472 SHEET 5 AA2 9 LEU A 379 GLY A 386 -1 N LEU A 384 O ARG A 392 SHEET 6 AA2 9 GLY A 363 THR A 371 -1 N GLN A 364 O ARG A 385 SHEET 7 AA2 9 VAL A 20 ILE A 35 -1 N GLY A 32 O LEU A 365 SHEET 8 AA2 9 VAL A 404 SER A 409 1 O ALA A 407 N LEU A 24 SHEET 9 AA2 9 PHE A 460 MET A 464 -1 O LEU A 462 N VAL A 406 SHEET 1 AA3 8 LEU A 165 LEU A 170 0 SHEET 2 AA3 8 LYS A 134 LEU A 139 1 N LEU A 139 O GLN A 169 SHEET 3 AA3 8 VAL A 74 GLY A 78 1 N LEU A 75 O LYS A 134 SHEET 4 AA3 8 GLY A 41 GLU A 45 1 N LEU A 42 O ARG A 76 SHEET 5 AA3 8 ILE A 324 HIS A 327 1 O PHE A 326 N SER A 43 SHEET 6 AA3 8 PHE A 283 ASN A 289 1 N THR A 288 O HIS A 327 SHEET 7 AA3 8 PHE A 237 TYR A 243 1 N ILE A 238 O ARG A 284 SHEET 8 AA3 8 ALA A 213 ALA A 218 1 N ASP A 216 O SER A 239 SHEET 1 AA4 2 THR A 85 TRP A 87 0 SHEET 2 AA4 2 GLU A 114 ILE A 116 1 O GLU A 114 N PHE A 86 SHEET 1 AA5 2 VAL A 337 THR A 340 0 SHEET 2 AA5 2 GLY A 344 ALA A 347 -1 O ILE A 346 N ALA A 338 LINK OE2 GLU A 287 C1 8I4 B 1 1555 1555 1.42 LINK O4 8I4 B 1 C1 NDG B 2 1555 1555 1.42 CISPEP 1 GLY A 214 PRO A 215 0 0.42 CRYST1 83.393 44.117 136.708 90.00 97.58 90.00 I 1 2 1 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 0.011991 0.000000 0.001596 0.00000 SCALE2 0.000000 0.022667 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007379 0.00000