HEADER LYASE 01-JUL-22 7YCD TITLE HYDROXYNITRILE LYASE FROM THE MILLIPEDE, OXIDUS GRACILIS BOUND WITH TITLE 2 (R)-(+)-ALPHA-HYDROXYBENZENE-ACETONITRILE COMPND MOL_ID: 1; COMPND 2 MOLECULE: HYDROXYNITRILE LYASE; COMPND 3 CHAIN: A, B, C, D; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: OXIDUS GRACILIS; SOURCE 3 ORGANISM_TAXID: 291247; SOURCE 4 GENE: OGRAHNL; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LYASE EXPDTA X-RAY DIFFRACTION AUTHOR S.CHAIKAEW,Y.WATANABE,D.ZHENG,F.MOTOJIMA,Y.ASANO REVDAT 2 19-JUN-24 7YCD 1 JRNL REVDAT 1 24-JAN-24 7YCD 0 JRNL AUTH S.CHAIKAEW,Y.WATANABE,D.ZHENG,F.MOTOJIMA,T.YAMAGUCHI,Y.ASANO JRNL TITL STRUCTURE-BASED SITE-DIRECTED MUTAGENESIS OF HYDROXYNITRILE JRNL TITL 2 LYASE FROM CYANOGENIC MILLIPEDE, OXIDUS GRACILIS FOR JRNL TITL 3 HYDROCYANATION AND HENRY REACTIONS. JRNL REF CHEMBIOCHEM V. 25 00118 2024 JRNL REFN ESSN 1439-7633 JRNL PMID 38526556 JRNL DOI 10.1002/CBIC.202400118 REMARK 2 REMARK 2 RESOLUTION. 2.01 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0352 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) : 2.01 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 74350 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING + TEST SET) : NULL REMARK 3 R VALUE (WORKING SET) : 0.202 REMARK 3 FREE R VALUE : 0.233 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.896 REMARK 3 FREE R VALUE TEST SET COUNT : 3640 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) : 2.01 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.06 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5093 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.27 REMARK 3 BIN R VALUE (WORKING SET) : 0.3360 REMARK 3 BIN FREE R VALUE SET COUNT : 278 REMARK 3 BIN FREE R VALUE : 0.3450 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5058 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 110 REMARK 3 SOLVENT ATOMS : 342 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.59 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.78200 REMARK 3 B22 (A**2) : 0.78200 REMARK 3 B33 (A**2) : -2.53800 REMARK 3 B12 (A**2) : 0.39100 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): 0.140 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.134 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.134 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 5.422 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.961 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5349 ; 0.008 ; 0.011 REMARK 3 BOND LENGTHS OTHERS (A): 4511 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7317 ; 1.546 ; 1.660 REMARK 3 BOND ANGLES OTHERS (DEGREES): 10609 ; 0.526 ; 1.553 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 656 ; 7.666 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 16 ;10.262 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 777 ;15.716 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 794 ; 0.069 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6088 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1024 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1015 ; 0.215 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 34 ; 0.184 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 2544 ; 0.180 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 329 ; 0.191 ; 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): 2618 ; 3.501 ; 4.477 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2618 ; 3.501 ; 4.477 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3270 ; 4.751 ; 6.696 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 3271 ; 4.751 ; 6.696 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2731 ; 4.537 ; 4.852 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2707 ; 4.337 ; 4.815 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 4045 ; 6.368 ; 7.117 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 4010 ; 6.171 ; 7.063 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 7YCD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 04-JUL-22. REMARK 100 THE DEPOSITION ID IS D_1300030653. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-AUG-17 REMARK 200 TEMPERATURE (KELVIN) : 293.15 REMARK 200 PH : 5.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 74395 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.010 REMARK 200 RESOLUTION RANGE LOW (A) : 64.940 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 3.100 REMARK 200 R MERGE (I) : 0.06600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.01 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.05 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.84600 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: NULL REMARK 200 STARTING MODEL: 6KFE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M BIS-TRIS, 2.0 M AMMONIUM REMARK 280 SULFATE, INCUBATED IN 25% (V/V) GLYCEROL WITH A DROP OF BA AND REMARK 280 2M POTASSIUM CYANIDE, PH 5.5, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 64.93500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 64.93500 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 64.93500 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 8600 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 26600 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -132.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 384 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 385 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 386 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 -17 REMARK 465 LEU A -16 REMARK 465 TYR A -15 REMARK 465 TYR A -14 REMARK 465 VAL A -13 REMARK 465 SER A -12 REMARK 465 ILE A -11 REMARK 465 LEU A -10 REMARK 465 LEU A -9 REMARK 465 MET A -8 REMARK 465 ALA A -7 REMARK 465 VAL A -6 REMARK 465 TYR A -5 REMARK 465 ALA A -4 REMARK 465 VAL A -3 REMARK 465 ALA A -2 REMARK 465 VAL A -1 REMARK 465 ALA A 0 REMARK 465 ASP A 1 REMARK 465 GLU A 2 REMARK 465 ASP A 3 REMARK 465 PRO A 4 REMARK 465 MET B -17 REMARK 465 LEU B -16 REMARK 465 TYR B -15 REMARK 465 TYR B -14 REMARK 465 VAL B -13 REMARK 465 SER B -12 REMARK 465 ILE B -11 REMARK 465 LEU B -10 REMARK 465 LEU B -9 REMARK 465 MET B -8 REMARK 465 ALA B -7 REMARK 465 VAL B -6 REMARK 465 TYR B -5 REMARK 465 ALA B -4 REMARK 465 VAL B -3 REMARK 465 ALA B -2 REMARK 465 VAL B -1 REMARK 465 ALA B 0 REMARK 465 ASP B 1 REMARK 465 GLU B 2 REMARK 465 MET C -17 REMARK 465 LEU C -16 REMARK 465 TYR C -15 REMARK 465 TYR C -14 REMARK 465 VAL C -13 REMARK 465 SER C -12 REMARK 465 ILE C -11 REMARK 465 LEU C -10 REMARK 465 LEU C -9 REMARK 465 MET C -8 REMARK 465 ALA C -7 REMARK 465 VAL C -6 REMARK 465 TYR C -5 REMARK 465 ALA C -4 REMARK 465 VAL C -3 REMARK 465 ALA C -2 REMARK 465 VAL C -1 REMARK 465 ALA C 0 REMARK 465 ASP C 1 REMARK 465 GLU C 2 REMARK 465 ASP C 3 REMARK 465 MET D -17 REMARK 465 LEU D -16 REMARK 465 TYR D -15 REMARK 465 TYR D -14 REMARK 465 VAL D -13 REMARK 465 SER D -12 REMARK 465 ILE D -11 REMARK 465 LEU D -10 REMARK 465 LEU D -9 REMARK 465 MET D -8 REMARK 465 ALA D -7 REMARK 465 VAL D -6 REMARK 465 TYR D -5 REMARK 465 ALA D -4 REMARK 465 VAL D -3 REMARK 465 ALA D -2 REMARK 465 VAL D -1 REMARK 465 ALA D 0 REMARK 465 ASP D 1 REMARK 465 GLU D 2 REMARK 465 ASP D 3 REMARK 465 PRO D 4 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 MET A 5 CE REMARK 470 MET B 5 CE REMARK 470 MET C 5 CE REMARK 470 MET D 5 CE 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 HH TYR D 96 HG2 GLN D 133 1.10 REMARK 500 HD1 HIS A 160 O HOH A 302 1.27 REMARK 500 HE21 GLN A 135 O HOH A 301 1.32 REMARK 500 HH12 ARG B 42 H7 MXN B 401 1.34 REMARK 500 H ASN C 155 O HOH C 303 1.48 REMARK 500 H GLY A 114 O HOH A 308 1.60 REMARK 500 NE2 GLN A 135 O HOH A 301 1.95 REMARK 500 O HOH C 310 O HOH C 372 2.06 REMARK 500 O HOH C 336 O HOH C 346 2.09 REMARK 500 ND1 HIS A 160 O HOH A 302 2.14 REMARK 500 O HOH B 511 O HOH B 584 2.15 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 LEU A 33 -69.19 -93.83 REMARK 500 ASN A 145 -10.37 89.03 REMARK 500 LEU B 33 -66.30 -91.29 REMARK 500 ASN B 145 -0.23 80.41 REMARK 500 ASN C 145 -12.76 96.21 REMARK 500 LEU D 33 -73.33 -95.01 REMARK 500 ASN D 76 41.98 77.60 REMARK 500 ASN D 145 0.78 89.78 REMARK 500 ASN D 155 61.29 -117.60 REMARK 500 PRO D 157 153.38 -49.63 REMARK 500 HIS D 160 52.26 -140.55 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 ARG C 65 0.09 SIDE CHAIN REMARK 500 ARG D 42 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF1 7YCD A -17 166 UNP A0A2Z5XCT7_9MYRI DBREF2 7YCD A A0A2Z5XCT7 1 184 DBREF1 7YCD B -17 166 UNP A0A2Z5XCT7_9MYRI DBREF2 7YCD B A0A2Z5XCT7 1 184 DBREF1 7YCD C -17 166 UNP A0A2Z5XCT7_9MYRI DBREF2 7YCD C A0A2Z5XCT7 1 184 DBREF1 7YCD D -17 166 UNP A0A2Z5XCT7_9MYRI DBREF2 7YCD D A0A2Z5XCT7 1 184 SEQRES 1 A 184 MET LEU TYR TYR VAL SER ILE LEU LEU MET ALA VAL TYR SEQRES 2 A 184 ALA VAL ALA VAL ALA ASP GLU ASP PRO MET THR CYS ASP SEQRES 3 A 184 LYS LEU PRO LYS VAL PRO VAL PRO PRO LEU GLU GLU PHE SEQRES 4 A 184 ILE LYS SER ASN PRO LEU GLN PHE ALA TYR VAL LEU THR SEQRES 5 A 184 ASP THR PHE ASP CYS THR THR ARG VAL TYR VAL GLN PRO SEQRES 6 A 184 ALA ARG LEU SER PRO ASN GLN ALA ALA THR ALA LEU ASP SEQRES 7 A 184 ILE ARG GLY SER ARG ILE ILE THR ASN ASP PHE VAL GLY SEQRES 8 A 184 GLY PRO ASN ASN SER ALA ILE LEU ASN ASN CYS THR THR SEQRES 9 A 184 GLY GLU LYS ALA THR TRP TYR PHE GLN TYR THR ASN LEU SEQRES 10 A 184 ASN THR PRO ASN GLY SER SER TYR CYS ALA TYR THR CYS SEQRES 11 A 184 ASN GLY GLU GLU ILE ALA GLU TYR LYS CYS ALA ASN ASN SEQRES 12 A 184 ASN ASN GLY THR ASP PRO LEU GLN LYS GLN ALA VAL GLU SEQRES 13 A 184 VAL ALA LYS LYS VAL PRO ASN GLY ASP LYS ILE HIS TYR SEQRES 14 A 184 ALA LEU ASP ASN CYS PRO GLU HIS HIS GLY CYS PHE ALA SEQRES 15 A 184 PHE TYR SEQRES 1 B 184 MET LEU TYR TYR VAL SER ILE LEU LEU MET ALA VAL TYR SEQRES 2 B 184 ALA VAL ALA VAL ALA ASP GLU ASP PRO MET THR CYS ASP SEQRES 3 B 184 LYS LEU PRO LYS VAL PRO VAL PRO PRO LEU GLU GLU PHE SEQRES 4 B 184 ILE LYS SER ASN PRO LEU GLN PHE ALA TYR VAL LEU THR SEQRES 5 B 184 ASP THR PHE ASP CYS THR THR ARG VAL TYR VAL GLN PRO SEQRES 6 B 184 ALA ARG LEU SER PRO ASN GLN ALA ALA THR ALA LEU ASP SEQRES 7 B 184 ILE ARG GLY SER ARG ILE ILE THR ASN ASP PHE VAL GLY SEQRES 8 B 184 GLY PRO ASN ASN SER ALA ILE LEU ASN ASN CYS THR THR SEQRES 9 B 184 GLY GLU LYS ALA THR TRP TYR PHE GLN TYR THR ASN LEU SEQRES 10 B 184 ASN THR PRO ASN GLY SER SER TYR CYS ALA TYR THR CYS SEQRES 11 B 184 ASN GLY GLU GLU ILE ALA GLU TYR LYS CYS ALA ASN ASN SEQRES 12 B 184 ASN ASN GLY THR ASP PRO LEU GLN LYS GLN ALA VAL GLU SEQRES 13 B 184 VAL ALA LYS LYS VAL PRO ASN GLY ASP LYS ILE HIS TYR SEQRES 14 B 184 ALA LEU ASP ASN CYS PRO GLU HIS HIS GLY CYS PHE ALA SEQRES 15 B 184 PHE TYR SEQRES 1 C 184 MET LEU TYR TYR VAL SER ILE LEU LEU MET ALA VAL TYR SEQRES 2 C 184 ALA VAL ALA VAL ALA ASP GLU ASP PRO MET THR CYS ASP SEQRES 3 C 184 LYS LEU PRO LYS VAL PRO VAL PRO PRO LEU GLU GLU PHE SEQRES 4 C 184 ILE LYS SER ASN PRO LEU GLN PHE ALA TYR VAL LEU THR SEQRES 5 C 184 ASP THR PHE ASP CYS THR THR ARG VAL TYR VAL GLN PRO SEQRES 6 C 184 ALA ARG LEU SER PRO ASN GLN ALA ALA THR ALA LEU ASP SEQRES 7 C 184 ILE ARG GLY SER ARG ILE ILE THR ASN ASP PHE VAL GLY SEQRES 8 C 184 GLY PRO ASN ASN SER ALA ILE LEU ASN ASN CYS THR THR SEQRES 9 C 184 GLY GLU LYS ALA THR TRP TYR PHE GLN TYR THR ASN LEU SEQRES 10 C 184 ASN THR PRO ASN GLY SER SER TYR CYS ALA TYR THR CYS SEQRES 11 C 184 ASN GLY GLU GLU ILE ALA GLU TYR LYS CYS ALA ASN ASN SEQRES 12 C 184 ASN ASN GLY THR ASP PRO LEU GLN LYS GLN ALA VAL GLU SEQRES 13 C 184 VAL ALA LYS LYS VAL PRO ASN GLY ASP LYS ILE HIS TYR SEQRES 14 C 184 ALA LEU ASP ASN CYS PRO GLU HIS HIS GLY CYS PHE ALA SEQRES 15 C 184 PHE TYR SEQRES 1 D 184 MET LEU TYR TYR VAL SER ILE LEU LEU MET ALA VAL TYR SEQRES 2 D 184 ALA VAL ALA VAL ALA ASP GLU ASP PRO MET THR CYS ASP SEQRES 3 D 184 LYS LEU PRO LYS VAL PRO VAL PRO PRO LEU GLU GLU PHE SEQRES 4 D 184 ILE LYS SER ASN PRO LEU GLN PHE ALA TYR VAL LEU THR SEQRES 5 D 184 ASP THR PHE ASP CYS THR THR ARG VAL TYR VAL GLN PRO SEQRES 6 D 184 ALA ARG LEU SER PRO ASN GLN ALA ALA THR ALA LEU ASP SEQRES 7 D 184 ILE ARG GLY SER ARG ILE ILE THR ASN ASP PHE VAL GLY SEQRES 8 D 184 GLY PRO ASN ASN SER ALA ILE LEU ASN ASN CYS THR THR SEQRES 9 D 184 GLY GLU LYS ALA THR TRP TYR PHE GLN TYR THR ASN LEU SEQRES 10 D 184 ASN THR PRO ASN GLY SER SER TYR CYS ALA TYR THR CYS SEQRES 11 D 184 ASN GLY GLU GLU ILE ALA GLU TYR LYS CYS ALA ASN ASN SEQRES 12 D 184 ASN ASN GLY THR ASP PRO LEU GLN LYS GLN ALA VAL GLU SEQRES 13 D 184 VAL ALA LYS LYS VAL PRO ASN GLY ASP LYS ILE HIS TYR SEQRES 14 D 184 ALA LEU ASP ASN CYS PRO GLU HIS HIS GLY CYS PHE ALA SEQRES 15 D 184 PHE TYR HET MXN A 201 17 HET MXN A 202 17 HET SO4 A 203 5 HET SO4 A 204 5 HET MXN B 401 17 HET MXN B 402 17 HET SO4 B 403 5 HET SO4 B 404 5 HET MXN C 201 17 HET MXN C 202 17 HET SO4 C 203 5 HET MXN D 201 17 HET MXN D 202 17 HET SO4 D 203 5 HETNAM MXN (2R)-HYDROXY(PHENYL)ETHANENITRILE HETNAM SO4 SULFATE ION HETSYN MXN (R)-MANDELONITRILE FORMUL 5 MXN 8(C8 H7 N O) FORMUL 7 SO4 6(O4 S 2-) FORMUL 19 HOH *342(H2 O) HELIX 1 AA1 THR A 6 LEU A 10 5 5 HELIX 2 AA2 PRO A 17 ASN A 25 1 9 HELIX 3 AA3 ASP A 130 LYS A 142 1 13 HELIX 4 AA4 ASN A 145 ILE A 149 5 5 HELIX 5 AA5 THR B 6 LEU B 10 5 5 HELIX 6 AA6 PRO B 17 LYS B 23 1 7 HELIX 7 AA7 THR B 34 ASP B 38 5 5 HELIX 8 AA8 PRO B 75 ASN B 77 5 3 HELIX 9 AA9 ASP B 130 LYS B 142 1 13 HELIX 10 AB1 ASN B 145 ILE B 149 5 5 HELIX 11 AB2 THR C 6 LEU C 10 5 5 HELIX 12 AB3 PRO C 17 ASN C 25 1 9 HELIX 13 AB4 THR C 34 ASP C 38 5 5 HELIX 14 AB5 ASP C 130 LYS C 142 1 13 HELIX 15 AB6 ASN C 145 ILE C 149 5 5 HELIX 16 AB7 THR D 6 LEU D 10 5 5 HELIX 17 AB8 PRO D 17 SER D 24 1 8 HELIX 18 AB9 THR D 34 ASP D 38 5 5 HELIX 19 AC1 ASP D 130 LYS D 142 1 13 SHEET 1 AA110 HIS A 150 TYR A 151 0 SHEET 2 AA110 LEU A 27 VAL A 32 -1 N VAL A 32 O HIS A 150 SHEET 3 AA110 GLU A 116 ASN A 124 -1 O CYS A 122 N TYR A 31 SHEET 4 AA110 GLY A 104 ASN A 113 -1 N ASN A 113 O GLU A 116 SHEET 5 AA110 LYS A 89 THR A 101 -1 N ASN A 98 O SER A 106 SHEET 6 AA110 SER A 78 ASN A 83 -1 N ALA A 79 O TRP A 92 SHEET 7 AA110 ARG A 65 GLY A 74 -1 N VAL A 72 O ILE A 80 SHEET 8 AA110 ALA A 56 ARG A 62 -1 N ALA A 58 O ASN A 69 SHEET 9 AA110 THR A 41 VAL A 45 -1 N THR A 41 O ILE A 61 SHEET 10 AA110 LEU A 27 VAL A 32 -1 N LEU A 27 O ARG A 42 SHEET 1 AA210 HIS B 150 TYR B 151 0 SHEET 2 AA210 LEU B 27 VAL B 32 -1 N VAL B 32 O HIS B 150 SHEET 3 AA210 GLU B 116 ASN B 124 -1 O ASN B 124 N GLN B 28 SHEET 4 AA210 GLY B 104 ASN B 113 -1 N ASN B 113 O GLU B 116 SHEET 5 AA210 LYS B 89 THR B 101 -1 N GLN B 95 O CYS B 108 SHEET 6 AA210 SER B 78 ASN B 83 -1 N LEU B 81 O ALA B 90 SHEET 7 AA210 ARG B 65 GLY B 74 -1 N VAL B 72 O ILE B 80 SHEET 8 AA210 ALA B 56 ARG B 62 -1 N ASP B 60 O ILE B 67 SHEET 9 AA210 THR B 41 VAL B 45 -1 N THR B 41 O ILE B 61 SHEET 10 AA210 LEU B 27 VAL B 32 -1 N LEU B 27 O ARG B 42 SHEET 1 AA310 HIS C 150 TYR C 151 0 SHEET 2 AA310 LEU C 27 VAL C 32 -1 N VAL C 32 O HIS C 150 SHEET 3 AA310 GLU C 116 ASN C 124 -1 O CYS C 122 N ALA C 30 SHEET 4 AA310 GLY C 104 ASN C 113 -1 N ASN C 113 O GLU C 116 SHEET 5 AA310 LYS C 89 THR C 101 -1 N ASN C 98 O SER C 106 SHEET 6 AA310 SER C 78 ASN C 83 -1 N LEU C 81 O ALA C 90 SHEET 7 AA310 ARG C 65 GLY C 74 -1 N GLY C 74 O SER C 78 SHEET 8 AA310 ALA C 56 ARG C 62 -1 N ALA C 58 O ASN C 69 SHEET 9 AA310 THR C 41 VAL C 45 -1 N VAL C 43 O LEU C 59 SHEET 10 AA310 LEU C 27 VAL C 32 -1 N LEU C 27 O ARG C 42 SHEET 1 AA410 HIS D 150 TYR D 151 0 SHEET 2 AA410 LEU D 27 VAL D 32 -1 N VAL D 32 O HIS D 150 SHEET 3 AA410 GLU D 116 ASN D 124 -1 O CYS D 122 N TYR D 31 SHEET 4 AA410 GLY D 104 ASN D 113 -1 N ASN D 113 O GLU D 116 SHEET 5 AA410 LYS D 89 THR D 101 -1 N ASN D 98 O SER D 106 SHEET 6 AA410 SER D 78 ASN D 83 -1 N ALA D 79 O TRP D 92 SHEET 7 AA410 ARG D 65 GLY D 74 -1 N VAL D 72 O ILE D 80 SHEET 8 AA410 ALA D 56 ARG D 62 -1 N ASP D 60 O ILE D 67 SHEET 9 AA410 THR D 41 VAL D 45 -1 N VAL D 45 O THR D 57 SHEET 10 AA410 LEU D 27 VAL D 32 -1 N LEU D 27 O ARG D 42 SSBOND 1 CYS A 7 CYS A 112 1555 1555 2.06 SSBOND 2 CYS A 39 CYS A 156 1555 1555 2.06 SSBOND 3 CYS A 84 CYS C 162 1555 1555 2.09 SSBOND 4 CYS A 108 CYS A 122 1555 1555 2.10 SSBOND 5 CYS A 162 CYS C 84 1555 1555 2.09 SSBOND 6 CYS B 7 CYS B 112 1555 1555 2.12 SSBOND 7 CYS B 39 CYS B 156 1555 1555 2.05 SSBOND 8 CYS B 84 CYS D 162 1555 1555 2.07 SSBOND 9 CYS B 108 CYS B 122 1555 1555 2.07 SSBOND 10 CYS B 162 CYS D 84 1555 1555 2.07 SSBOND 11 CYS C 7 CYS C 112 1555 1555 2.06 SSBOND 12 CYS C 39 CYS C 156 1555 1555 2.04 SSBOND 13 CYS C 108 CYS C 122 1555 1555 2.09 SSBOND 14 CYS D 7 CYS D 112 1555 1555 2.08 SSBOND 15 CYS D 39 CYS D 156 1555 1555 2.07 SSBOND 16 CYS D 108 CYS D 122 1555 1555 2.07 CISPEP 1 ASN A 25 PRO A 26 0 -9.69 CISPEP 2 ASN B 25 PRO B 26 0 -18.07 CISPEP 3 ASN C 25 PRO C 26 0 -15.23 CISPEP 4 ASN D 25 PRO D 26 0 -15.42 CRYST1 123.430 123.430 129.870 90.00 90.00 120.00 P 63 24 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 0.008102 0.004678 0.000000 0.00000 SCALE2 0.000000 0.009355 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007700 0.00000