HEADER HYDROLASE 16-AUG-22 7YU2 TITLE STRUCTURE OF 6-AMINOHEXANOATE-OLIGOMER HYDROLASE NYLC, TITLE 2 D122G/H130Y/T267C MUTANT, HYDROXYLAMINE-TREATED COMPND MOL_ID: 1; COMPND 2 MOLECULE: 6-AMINOHEXANOATE-OLIGOMER ENDOHYDROLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 6-AMINOHEXANOATE OLIGOMER HYDROLASE,AHX ENDO-TYPE-OLIGOMER COMPND 5 HYDROLASE,NYLON HYDROLASE,NYLON OLIGOMER-DEGRADING ENZYME EIII, COMPND 6 NYLONASE; COMPND 7 EC: 3.5.1.117; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES; COMPND 10 OTHER_DETAILS: AUTHORS STATE THAT THE LONG GAP BETWEEN THE RESIDUES COMPND 11 IS DUE TO THE POST-TRANSLATIONAL AUTO-CLEAVAGE OF THE NASCENT COMPND 12 POLYPEPTIDE BETWEEN ASN266 AND THR267. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARTHROBACTER; SOURCE 3 ORGANISM_TAXID: 1663; SOURCE 4 STRAIN: K172; SOURCE 5 GENE: NYLC; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: JM109 KEYWDS NYLON OLIGOMER, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR S.NEGORO,Y.HIGUCHI REVDAT 3 29-NOV-23 7YU2 1 REMARK REVDAT 2 19-JUL-23 7YU2 1 COMPND JRNL REMARK REVDAT 1 29-MAR-23 7YU2 0 JRNL AUTH S.NEGORO,N.SHIBATA,D.I.KATO,Y.TANAKA,K.YASUHIRA,K.NAGAI, JRNL AUTH 2 S.OSHIMA,Y.FURUNO,R.YOKOYAMA,K.MIYAZAKI,M.TAKEO, JRNL AUTH 3 K.HENGPHASATPORN,Y.SHIGETA,Y.H.LEE,Y.HIGUCHI JRNL TITL X-RAY CRYSTALLOGRAPHIC AND MUTATIONAL ANALYSIS OF THE NYLC JRNL TITL 2 PRECURSOR: CATALYTIC MECHANISM OF AUTOCLEAVAGE AND SUBSTRATE JRNL TITL 3 HYDROLYSIS OF NYLON HYDROLASE. JRNL REF FEBS J. V. 290 3400 2023 JRNL REFN ISSN 1742-464X JRNL PMID 36799721 JRNL DOI 10.1111/FEBS.16755 REMARK 2 REMARK 2 RESOLUTION. 1.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0267 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) : 1.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.15 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 194260 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) : 0.116 REMARK 3 FREE R VALUE : 0.143 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 9810 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.21 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.24 REMARK 3 REFLECTION IN BIN (WORKING SET) : 12632 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.93 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE SET COUNT : 686 REMARK 3 BIN FREE R VALUE : 0.2660 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4877 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 63 REMARK 3 SOLVENT ATOMS : 627 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 16.96 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.54700 REMARK 3 B22 (A**2) : -1.27500 REMARK 3 B33 (A**2) : -0.27200 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): 0.030 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.032 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.023 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.221 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.985 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.980 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5434 ; 0.019 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 5142 ; 0.003 ; 0.015 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7425 ; 2.105 ; 1.643 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11813 ; 1.641 ; 1.577 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 750 ; 6.791 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 292 ;32.205 ;20.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 800 ;11.745 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 57 ;13.991 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 703 ; 0.124 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6421 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1309 ; 0.002 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1066 ; 0.244 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 177 ; 0.288 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2544 ; 0.177 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 443 ; 0.190 ; 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): 2840 ; 2.387 ; 1.448 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2839 ; 2.387 ; 1.448 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3573 ; 2.810 ; 2.178 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3574 ; 2.809 ; 2.178 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2590 ; 4.569 ; 1.866 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2579 ; 4.440 ; 1.847 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 3825 ; 4.982 ; 2.687 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3808 ; 4.782 ; 2.652 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): 10570 ; 7.498 ; 3.000 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 : BABINET MODEL PLUS MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THEIR REMARK 3 RIDING POSITIONS REMARK 4 REMARK 4 7YU2 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 18-AUG-22. REMARK 100 THE DEPOSITION ID IS D_1300031631. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-NOV-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL44XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9000 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX225HE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 194470 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.210 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 7.000 REMARK 200 R MERGE (I) : 0.06200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.2 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : 0.65000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.040 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: 3AXG REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1.4 M AMMONIUM SULFATE, 0.2 M SODIUM REMARK 280 CHLORIDE, 0.1 M HEPES PH 7.5., VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 283K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z 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 64.13100 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.13100 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 35.13500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 72.01100 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 35.13500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 72.01100 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 64.13100 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 35.13500 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 72.01100 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 64.13100 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 35.13500 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 72.01100 REMARK 290 SMTRY3 8 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 5530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24460 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -57.0 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 816 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 ASN A 2 REMARK 465 THR A 3 REMARK 465 THR A 4 REMARK 465 PRO A 5 REMARK 465 VAL A 6 REMARK 465 HIS A 7 REMARK 465 ALA A 8 REMARK 465 LEU A 9 REMARK 465 THR A 10 REMARK 465 ASP A 11 REMARK 465 ILE A 12 REMARK 465 ASP A 13 REMARK 465 GLY A 14 REMARK 465 GLY A 15 REMARK 465 ILE A 16 REMARK 465 ALA A 17 REMARK 465 VAL A 18 REMARK 465 PRO A 260 REMARK 465 VAL A 261 REMARK 465 THR A 262 REMARK 465 GLU A 263 REMARK 465 ALA A 264 REMARK 465 GLY A 265 REMARK 465 ASN A 266 REMARK 465 MET B 1 REMARK 465 ASN B 2 REMARK 465 THR B 3 REMARK 465 THR B 4 REMARK 465 PRO B 5 REMARK 465 VAL B 6 REMARK 465 HIS B 7 REMARK 465 ALA B 8 REMARK 465 LEU B 9 REMARK 465 THR B 10 REMARK 465 ASP B 11 REMARK 465 ILE B 12 REMARK 465 ASP B 13 REMARK 465 GLY B 14 REMARK 465 GLY B 15 REMARK 465 VAL B 261 REMARK 465 THR B 262 REMARK 465 GLU B 263 REMARK 465 ALA B 264 REMARK 465 GLY B 265 REMARK 465 ASN B 266 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 HD1 HIS B 245 H VAL B 247 1.20 REMARK 500 HD1 HIS B 102 H LEU B 139 1.22 REMARK 500 HD1 HIS A 245 H VAL A 247 1.22 REMARK 500 HG SER A 45 H GLY A 180 1.23 REMARK 500 HG SER B 45 H GLY B 180 1.23 REMARK 500 HD1 HIS A 102 H LEU A 139 1.24 REMARK 500 HE1 PHE B 30 OG SER B 149 1.28 REMARK 500 HH21 ARG A 163 O HOH A 501 1.33 REMARK 500 HH11 ARG B 206 OD1 ASP B 209 1.46 REMARK 500 HH22 ARG B 82 O3 SO4 B 404 1.53 REMARK 500 HH12 ARG A 163 O2 SO4 A 407 1.57 REMARK 500 O1 GOL B 401 O HOH B 501 1.87 REMARK 500 CE1 PHE B 30 OG SER B 149 2.00 REMARK 500 O HOH B 576 O HOH B 729 2.09 REMARK 500 NH2 ARG A 163 O HOH A 501 2.10 REMARK 500 NH1 ARG B 206 OD1 ASP B 209 2.10 REMARK 500 OD1 ASN A 284 O HOH A 502 2.10 REMARK 500 OE1 GLU A 67 O HOH A 503 2.12 REMARK 500 O HOH B 753 O HOH B 773 2.13 REMARK 500 O2 GOL B 401 O HOH B 502 2.15 REMARK 500 O VAL B 170 O HOH B 503 2.15 REMARK 500 O1 GOL A 401 O HOH A 504 2.17 REMARK 500 O HOH A 639 O HOH A 728 2.17 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 B 531 O HOH B 531 3554 2.16 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 PHE A 30 C PHE A 30 O 0.156 REMARK 500 GLU A 136 CD GLU A 136 OE2 0.105 REMARK 500 SER A 149 CB SER A 149 OG 0.093 REMARK 500 GLN A 239 CD GLN A 239 NE2 0.174 REMARK 500 GLU B 66 CD GLU B 66 OE1 0.124 REMARK 500 GLU B 136 CD GLU B 136 OE1 0.072 REMARK 500 GLY B 208 C GLY B 208 O 0.127 REMARK 500 GLU B 344 CD GLU B 344 OE2 -0.067 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 82 NE - CZ - NH1 ANGL. DEV. = -4.2 DEGREES REMARK 500 ARG A 88 NE - CZ - NH1 ANGL. DEV. = -3.4 DEGREES REMARK 500 CYS A 267 CB - CA - C ANGL. DEV. = -12.9 DEGREES REMARK 500 TYR B 65 CD1 - CE1 - CZ ANGL. DEV. = 6.7 DEGREES REMARK 500 ARG B 88 NE - CZ - NH1 ANGL. DEV. = -3.1 DEGREES REMARK 500 ARG B 88 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 ARG B 277 NE - CZ - NH1 ANGL. DEV. = 5.9 DEGREES REMARK 500 MET B 305 CG - SD - CE ANGL. DEV. = 10.1 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 ALA A 110 -151.80 52.77 REMARK 500 SER A 152 40.22 -105.61 REMARK 500 THR A 198 -101.91 -99.87 REMARK 500 LEU A 331 64.07 -115.82 REMARK 500 ASN A 334 -169.18 -161.09 REMARK 500 ALA B 110 -151.76 52.97 REMARK 500 THR B 198 -101.71 -101.53 REMARK 500 ASP B 209 -37.93 80.53 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 GLN A 239 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 ASP B 86 10.57 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 817 DISTANCE = 8.43 ANGSTROMS REMARK 525 HOH B 810 DISTANCE = 7.18 ANGSTROMS DBREF 7YU2 A 1 355 UNP Q79F77 NYLC_FLASK 1 355 DBREF 7YU2 B 1 355 UNP Q79F77 NYLC_FLASK 1 355 SEQADV 7YU2 GLY A 122 UNP Q79F77 ASP 122 ENGINEERED MUTATION SEQADV 7YU2 TYR A 130 UNP Q79F77 HIS 130 ENGINEERED MUTATION SEQADV 7YU2 CYS A 267 UNP Q79F77 THR 267 ENGINEERED MUTATION SEQADV 7YU2 GLY B 122 UNP Q79F77 ASP 122 ENGINEERED MUTATION SEQADV 7YU2 TYR B 130 UNP Q79F77 HIS 130 ENGINEERED MUTATION SEQADV 7YU2 CYS B 267 UNP Q79F77 THR 267 ENGINEERED MUTATION SEQRES 1 A 355 MET ASN THR THR PRO VAL HIS ALA LEU THR ASP ILE ASP SEQRES 2 A 355 GLY GLY ILE ALA VAL ASP PRO ALA PRO ARG LEU ALA GLY SEQRES 3 A 355 PRO PRO VAL PHE GLY GLY PRO GLY ASN ASP ALA PHE ASP SEQRES 4 A 355 LEU ALA PRO VAL ARG SER THR GLY ARG GLU MET LEU ARG SEQRES 5 A 355 PHE ASP PHE PRO GLY VAL SER ILE GLY ALA ALA HIS TYR SEQRES 6 A 355 GLU GLU GLY PRO THR GLY ALA THR VAL ILE HIS ILE PRO SEQRES 7 A 355 ALA GLY ALA ARG THR ALA VAL ASP ALA ARG GLY GLY ALA SEQRES 8 A 355 VAL GLY LEU SER GLY GLY TYR ASP PHE ASN HIS ALA ILE SEQRES 9 A 355 CYS LEU ALA GLY GLY ALA GLY TYR GLY LEU GLU ALA GLY SEQRES 10 A 355 ALA GLY VAL SER GLY ALA LEU LEU GLU ARG LEU GLU TYR SEQRES 11 A 355 ARG THR GLY PHE ALA GLU LEU GLN LEU VAL SER SER ALA SEQRES 12 A 355 VAL ILE TYR ASP PHE SER ALA ARG SER THR ALA VAL TYR SEQRES 13 A 355 PRO ASP LYS ALA LEU GLY ARG ALA ALA LEU GLU PHE ALA SEQRES 14 A 355 VAL PRO GLY GLU PHE PRO GLN GLY ARG ALA GLY ALA GLY SEQRES 15 A 355 MET SER ALA SER ALA GLY LYS VAL ASP TRP ASP ARG THR SEQRES 16 A 355 GLU ILE THR GLY GLN GLY ALA ALA PHE ARG ARG LEU GLY SEQRES 17 A 355 ASP VAL ARG ILE LEU ALA VAL VAL VAL PRO ASN PRO VAL SEQRES 18 A 355 GLY VAL ILE VAL ASP ARG ALA GLY THR VAL VAL ARG GLY SEQRES 19 A 355 ASN TYR ASP ALA GLN THR GLY VAL ARG ARG HIS PRO VAL SEQRES 20 A 355 PHE ASP TYR GLN GLU ALA PHE ALA GLU GLN VAL PRO PRO SEQRES 21 A 355 VAL THR GLU ALA GLY ASN CYS THR ILE SER ALA ILE VAL SEQRES 22 A 355 THR ASN VAL ARG MET SER PRO VAL GLU LEU ASN GLN PHE SEQRES 23 A 355 ALA LYS GLN VAL HIS SER SER MET HIS ARG GLY ILE GLN SEQRES 24 A 355 PRO PHE HIS THR ASP MET ASP GLY ASP THR LEU PHE ALA SEQRES 25 A 355 VAL THR THR ASP GLU ILE ASP LEU PRO THR THR PRO GLY SEQRES 26 A 355 SER SER ARG GLY ARG LEU SER VAL ASN ALA THR ALA LEU SEQRES 27 A 355 GLY ALA ILE ALA SER GLU VAL MET TRP ASP ALA VAL LEU SEQRES 28 A 355 GLU ALA GLY LYS SEQRES 1 B 355 MET ASN THR THR PRO VAL HIS ALA LEU THR ASP ILE ASP SEQRES 2 B 355 GLY GLY ILE ALA VAL ASP PRO ALA PRO ARG LEU ALA GLY SEQRES 3 B 355 PRO PRO VAL PHE GLY GLY PRO GLY ASN ASP ALA PHE ASP SEQRES 4 B 355 LEU ALA PRO VAL ARG SER THR GLY ARG GLU MET LEU ARG SEQRES 5 B 355 PHE ASP PHE PRO GLY VAL SER ILE GLY ALA ALA HIS TYR SEQRES 6 B 355 GLU GLU GLY PRO THR GLY ALA THR VAL ILE HIS ILE PRO SEQRES 7 B 355 ALA GLY ALA ARG THR ALA VAL ASP ALA ARG GLY GLY ALA SEQRES 8 B 355 VAL GLY LEU SER GLY GLY TYR ASP PHE ASN HIS ALA ILE SEQRES 9 B 355 CYS LEU ALA GLY GLY ALA GLY TYR GLY LEU GLU ALA GLY SEQRES 10 B 355 ALA GLY VAL SER GLY ALA LEU LEU GLU ARG LEU GLU TYR SEQRES 11 B 355 ARG THR GLY PHE ALA GLU LEU GLN LEU VAL SER SER ALA SEQRES 12 B 355 VAL ILE TYR ASP PHE SER ALA ARG SER THR ALA VAL TYR SEQRES 13 B 355 PRO ASP LYS ALA LEU GLY ARG ALA ALA LEU GLU PHE ALA SEQRES 14 B 355 VAL PRO GLY GLU PHE PRO GLN GLY ARG ALA GLY ALA GLY SEQRES 15 B 355 MET SER ALA SER ALA GLY LYS VAL ASP TRP ASP ARG THR SEQRES 16 B 355 GLU ILE THR GLY GLN GLY ALA ALA PHE ARG ARG LEU GLY SEQRES 17 B 355 ASP VAL ARG ILE LEU ALA VAL VAL VAL PRO ASN PRO VAL SEQRES 18 B 355 GLY VAL ILE VAL ASP ARG ALA GLY THR VAL VAL ARG GLY SEQRES 19 B 355 ASN TYR ASP ALA GLN THR GLY VAL ARG ARG HIS PRO VAL SEQRES 20 B 355 PHE ASP TYR GLN GLU ALA PHE ALA GLU GLN VAL PRO PRO SEQRES 21 B 355 VAL THR GLU ALA GLY ASN CYS THR ILE SER ALA ILE VAL SEQRES 22 B 355 THR ASN VAL ARG MET SER PRO VAL GLU LEU ASN GLN PHE SEQRES 23 B 355 ALA LYS GLN VAL HIS SER SER MET HIS ARG GLY ILE GLN SEQRES 24 B 355 PRO PHE HIS THR ASP MET ASP GLY ASP THR LEU PHE ALA SEQRES 25 B 355 VAL THR THR ASP GLU ILE ASP LEU PRO THR THR PRO GLY SEQRES 26 B 355 SER SER ARG GLY ARG LEU SER VAL ASN ALA THR ALA LEU SEQRES 27 B 355 GLY ALA ILE ALA SER GLU VAL MET TRP ASP ALA VAL LEU SEQRES 28 B 355 GLU ALA GLY LYS HET GOL A 401 14 HET GOL A 402 14 HET GOL A 403 14 HET GOL A 404 14 HET GOL A 405 14 HET SO4 A 406 5 HET SO4 A 407 5 HET GOL B 401 14 HET GOL B 402 14 HET GOL B 403 14 HET SO4 B 404 5 HETNAM GOL GLYCEROL HETNAM SO4 SULFATE ION HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 8(C3 H8 O3) FORMUL 8 SO4 3(O4 S 2-) FORMUL 14 HOH *627(H2 O) HELIX 1 AA1 GLY A 34 PHE A 38 5 5 HELIX 2 AA2 GLY A 109 GLY A 113 5 5 HELIX 3 AA3 LEU A 114 LEU A 128 1 15 HELIX 4 AA4 GLY A 133 LEU A 137 5 5 HELIX 5 AA5 ASP A 147 ARG A 151 5 5 HELIX 6 AA6 ASP A 158 PHE A 168 1 11 HELIX 7 AA7 ALA A 179 MET A 183 5 5 HELIX 8 AA8 ASP A 191 THR A 195 5 5 HELIX 9 AA9 HIS A 245 VAL A 258 1 14 HELIX 10 AB1 SER A 279 MET A 294 1 16 HELIX 11 AB2 ASN A 334 LYS A 355 1 22 HELIX 12 AB3 GLY B 34 PHE B 38 5 5 HELIX 13 AB4 GLY B 109 GLY B 113 5 5 HELIX 14 AB5 LEU B 114 LEU B 128 1 15 HELIX 15 AB6 GLY B 133 LEU B 137 5 5 HELIX 16 AB7 ASP B 147 ARG B 151 5 5 HELIX 17 AB8 ASP B 158 PHE B 168 1 11 HELIX 18 AB9 ALA B 179 MET B 183 5 5 HELIX 19 AC1 ASP B 191 THR B 195 5 5 HELIX 20 AC2 HIS B 245 VAL B 258 1 14 HELIX 21 AC3 SER B 279 MET B 294 1 16 HELIX 22 AC4 ASN B 334 LYS B 355 1 22 SHEET 1 AA1 4 VAL A 43 ARG A 44 0 SHEET 2 AA1 4 SER A 59 TYR A 65 -1 O HIS A 64 N VAL A 43 SHEET 3 AA1 4 THR A 70 ARG A 88 -1 O VAL A 74 N GLY A 61 SHEET 4 AA1 4 VAL A 170 PRO A 171 0 SHEET 1 AA2 9 LEU A 94 SER A 95 0 SHEET 2 AA2 9 VAL A 140 VAL A 144 -1 O SER A 142 N SER A 95 SHEET 3 AA2 9 PHE A 100 ALA A 107 1 N CYS A 105 O SER A 141 SHEET 4 AA2 9 THR A 70 ARG A 88 -1 N THR A 73 O LEU A 106 SHEET 5 AA2 9 SER A 59 TYR A 65 -1 N GLY A 61 O VAL A 74 SHEET 6 AA2 9 ASP A 308 ILE A 318 0 SHEET 7 AA2 9 THR A 268 VAL A 276 1 N ILE A 272 O VAL A 313 SHEET 8 AA2 9 VAL A 210 PRO A 218 -1 N LEU A 213 O VAL A 273 SHEET 9 AA2 9 GLY A 201 LEU A 207 -1 N ALA A 203 O ALA A 214 SHEET 1 AA3 2 GLU A 49 ARG A 52 0 SHEET 2 AA3 2 GLU A 173 GLN A 176 -1 O PHE A 174 N LEU A 51 SHEET 1 AA4 2 SER A 186 ALA A 187 0 SHEET 2 AA4 2 GLU A 196 ILE A 197 -1 O GLU A 196 N ALA A 187 SHEET 1 AA5 3 VAL A 231 ARG A 233 0 SHEET 2 AA5 3 VAL A 223 VAL A 225 -1 N ILE A 224 O ARG A 233 SHEET 3 AA5 3 ILE A 298 GLN A 299 -1 O GLN A 299 N VAL A 223 SHEET 1 AA6 4 VAL B 43 ARG B 44 0 SHEET 2 AA6 4 SER B 59 TYR B 65 -1 O HIS B 64 N VAL B 43 SHEET 3 AA6 4 THR B 70 ARG B 88 -1 O VAL B 74 N GLY B 61 SHEET 4 AA6 4 VAL B 170 PRO B 171 0 SHEET 1 AA7 9 LEU B 94 SER B 95 0 SHEET 2 AA7 9 VAL B 140 VAL B 144 -1 O SER B 142 N SER B 95 SHEET 3 AA7 9 PHE B 100 ALA B 107 1 N CYS B 105 O SER B 141 SHEET 4 AA7 9 THR B 70 ARG B 88 -1 N THR B 73 O LEU B 106 SHEET 5 AA7 9 SER B 59 TYR B 65 -1 N GLY B 61 O VAL B 74 SHEET 6 AA7 9 ASP B 308 ILE B 318 0 SHEET 7 AA7 9 THR B 268 VAL B 276 1 N ILE B 272 O VAL B 313 SHEET 8 AA7 9 VAL B 210 PRO B 218 -1 N LEU B 213 O VAL B 273 SHEET 9 AA7 9 GLY B 201 LEU B 207 -1 N ALA B 203 O ALA B 214 SHEET 1 AA8 2 GLU B 49 ARG B 52 0 SHEET 2 AA8 2 GLU B 173 GLN B 176 -1 O PHE B 174 N LEU B 51 SHEET 1 AA9 2 SER B 186 ALA B 187 0 SHEET 2 AA9 2 GLU B 196 ILE B 197 -1 O GLU B 196 N ALA B 187 SHEET 1 AB1 3 VAL B 231 ARG B 233 0 SHEET 2 AB1 3 VAL B 223 VAL B 225 -1 N ILE B 224 O ARG B 233 SHEET 3 AB1 3 ILE B 298 GLN B 299 -1 O GLN B 299 N VAL B 223 CISPEP 1 GLY A 68 PRO A 69 0 -5.95 CISPEP 2 VAL A 258 PRO A 259 0 3.13 CISPEP 3 GLN A 299 PRO A 300 0 -15.25 CISPEP 4 GLY B 68 PRO B 69 0 -10.05 CISPEP 5 GLN B 299 PRO B 300 0 -16.20 CRYST1 70.270 144.022 128.262 90.00 90.00 90.00 C 2 2 21 16 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 0.014231 0.000000 0.000000 0.00000 SCALE2 0.000000 0.006943 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007797 0.00000