HEADER LYASE 04-JUN-23 8JM3 TITLE ENDO-DEGLYCOSYLATED HYDROXYNITRILE LYASE ISOZYME 5 MUTANT L331A FROM TITLE 2 PRUNUS COMMUNIS COMPLEXED WITH 4H-BENZO[D][1,3]DIOXINE-6-CARBALDEHYDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: (R)-MANDELONITRILE LYASE; COMPND 3 CHAIN: A; COMPND 4 EC: 4.1.2.10; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES; COMPND 7 OTHER_DETAILS: AUTHOR STATED THE SEQUENCE REFERENCE IS GENBANK COMPND 8 AAP84580.1, AND THE INITIAL SIGNAL PEPTIDE (MET1 TO SER27) WAS COMPND 9 EXCHANGED INTO YEAST α-FACTOR SUBJECTED TO CLEAVAGE DURING COMPND 10 EXTRACELLULAR EXPRESSION. SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PRUNUS DULCIS; SOURCE 3 ORGANISM_COMMON: ALMOND; SOURCE 4 ORGANISM_TAXID: 3755; SOURCE 5 GENE: ALMOND_2B028509; SOURCE 6 EXPRESSION_SYSTEM: KOMAGATAELLA PASTORIS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 4922; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: X33 KEYWDS HYDROXYNITRILE LYASE, FAD, HYDROCYNANATION, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR Y.C.ZHENG,F.L.LI,H.L.YU,J.H.XU REVDAT 3 07-JAN-26 8JM3 1 AUTHOR JRNL REVDAT 2 06-NOV-24 8JM3 1 REMARK REVDAT 1 12-JUN-24 8JM3 0 JRNL AUTH Y.C.ZHENG,Y.MAO,Q.GENG,F.L.LI,X.D.KONG,Y.K.QI,L.ZHANG, JRNL AUTH 2 Q.CHEN,Z.J.ZHANG,R.HONG,Y.L.ZHAO,H.L.YU,J.H.XU JRNL TITL FLIPPING OF A NON-PRODUCTIVE SUBSTRATE BINDING CONFORMATION JRNL TITL 2 FACILITATES HYDROXYNITRILE LYASE CATALYZED HYDROCYANATION. JRNL REF ANGEW.CHEM.INT.ED.ENGL. V. 64 15778 2025 JRNL REFN ESSN 1521-3773 JRNL PMID 41137404 JRNL DOI 10.1002/ANIE.202515778 REMARK 2 REMARK 2 RESOLUTION. 1.90 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 : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 39.46 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 44669 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) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.159 REMARK 3 FREE R VALUE : 0.195 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 2421 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3045 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 94.23 REMARK 3 BIN R VALUE (WORKING SET) : 0.2060 REMARK 3 BIN FREE R VALUE SET COUNT : 173 REMARK 3 BIN FREE R VALUE : 0.2210 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3948 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 161 REMARK 3 SOLVENT ATOMS : 296 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.15 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.18000 REMARK 3 B22 (A**2) : -0.95000 REMARK 3 B33 (A**2) : 1.13000 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): 0.125 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.119 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.081 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.803 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.968 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.955 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4222 ; 0.011 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 3818 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5779 ; 1.717 ; 1.674 REMARK 3 BOND ANGLES OTHERS (DEGREES): 8810 ; 1.422 ; 1.598 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 513 ; 7.501 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 202 ;34.704 ;23.317 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 613 ;12.446 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 18 ;16.081 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 564 ; 0.084 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4805 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 945 ; 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): 2055 ; 2.525 ; 2.865 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2054 ; 2.521 ; 2.863 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2564 ; 3.247 ; 4.281 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2565 ; 3.246 ; 4.283 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2167 ; 3.484 ; 3.246 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2164 ; 3.479 ; 3.240 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3209 ; 5.047 ; 4.737 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4736 ; 6.170 ;35.101 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4737 ; 6.177 ;35.108 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 8JM3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBC ON 08-JUN-23. REMARK 100 THE DEPOSITION ID IS D_1300038207. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-MAY-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.25-8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97891 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 : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 47153 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 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 (%) : 99.9 REMARK 200 DATA REDUNDANCY : 10.90 REMARK 200 R MERGE (I) : 0.11400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 5.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 11.20 REMARK 200 R MERGE FOR SHELL (I) : 0.83900 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.88 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: TRIS-BICINE, 100 MM, PH 8.25; CACL2, REMARK 280 60 MM; MGCL2, 60 MM; PEG 500MME, 24%, V/V; PEG 20000, 12%, W/V, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 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 24.82400 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 64.86200 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 45.85650 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 64.86200 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 24.82400 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 45.85650 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 18570 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 15.0 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 ILE A -7 REMARK 465 ASP A -6 REMARK 465 HIS A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 SER A 224 REMARK 465 ASN A 225 REMARK 465 THR A 226 REMARK 465 SER A 227 REMARK 465 GLU A 439 REMARK 465 ASN A 440 REMARK 465 ILE A 520 REMARK 465 ARG A 521 REMARK 465 LEU A 522 REMARK 465 GLU A 523 REMARK 465 ALA A 524 REMARK 465 ILE A 525 REMARK 465 HIS A 526 REMARK 465 ASN A 527 REMARK 465 ILE A 528 REMARK 465 GLN A 529 REMARK 465 GLU A 530 REMARK 465 SER A 531 REMARK 465 MET A 532 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 ND2 ASN A 151 O HOH A 701 1.95 REMARK 500 O HOH A 966 O HOH A 968 2.01 REMARK 500 O HOH A 985 O HOH A 996 2.07 REMARK 500 O HOH A 970 O HOH A 989 2.11 REMARK 500 O HOH A 846 O HOH A 960 2.14 REMARK 500 OE2 GLU A 160 O HOH A 702 2.16 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 962 O HOH A 974 3544 2.12 REMARK 500 O HOH A 909 O HOH A 938 4455 2.14 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 101 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG A 101 NE - CZ - NH2 ANGL. DEV. = -4.5 DEGREES REMARK 500 TYR A 503 CB - CG - CD2 ANGL. DEV. = 4.2 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 ILE A 102 148.00 -171.51 REMARK 500 ASN A 118 119.38 -35.94 REMARK 500 SER A 342 -9.64 83.28 REMARK 500 THR A 442 22.27 -146.97 REMARK 500 LYS A 469 -59.10 -122.80 REMARK 500 ASP A 487 -170.51 172.40 REMARK 500 ASN A 496 -168.52 -177.90 REMARK 500 REMARK 500 REMARK: NULL DBREF 8JM3 A -7 532 PDB 8JM3 8JM3 -7 532 SEQRES 1 A 540 ILE ASP HIS HIS HIS HIS HIS HIS LEU ALA ASN THR SER SEQRES 2 A 540 ALA HIS ASP PHE SER TYR LEU LYS PHE VAL TYR ASN ALA SEQRES 3 A 540 THR ASP THR SER LEU GLU GLY SER TYR ASP TYR ILE VAL SEQRES 4 A 540 ILE GLY GLY GLY THR SER GLY CYS PRO LEU ALA ALA THR SEQRES 5 A 540 LEU SER GLU LYS TYR LYS VAL LEU LEU LEU GLU ARG GLY SEQRES 6 A 540 THR ILE ALA THR GLU TYR PRO ASN THR LEU THR ALA ASP SEQRES 7 A 540 GLY PHE ALA TYR ASN LEU GLN GLN GLN ASP ASP GLY LYS SEQRES 8 A 540 THR PRO VAL GLU ARG PHE VAL SER GLU ASP GLY ILE ASP SEQRES 9 A 540 ASN VAL ARG ALA ARG ILE LEU GLY GLY THR THR ILE ILE SEQRES 10 A 540 ASN ALA GLY VAL TYR ALA ARG ALA ASN ILE SER PHE TYR SEQRES 11 A 540 SER GLN THR GLY ILE GLU TRP ASP LEU ASP LEU VAL ASN SEQRES 12 A 540 LYS THR TYR GLU TRP VAL GLU ASP ALA ILE VAL VAL LYS SEQRES 13 A 540 PRO ASN ASN GLN SER TRP GLN SER VAL ILE GLY GLU GLY SEQRES 14 A 540 PHE LEU GLU ALA GLY ILE LEU PRO ASP ASN GLY PHE SER SEQRES 15 A 540 LEU ASP HIS GLU ALA GLY THR ARG LEU THR GLY SER THR SEQRES 16 A 540 PHE ASP ASN ASN GLY THR ARG HIS ALA ALA ASP GLU LEU SEQRES 17 A 540 LEU ASN LYS GLY ASP PRO ASN ASN LEU LEU VAL ALA VAL SEQRES 18 A 540 GLN ALA SER VAL GLU LYS ILE LEU PHE SER SER ASN THR SEQRES 19 A 540 SER ASN LEU SER ALA ILE GLY VAL ILE TYR THR ASP SER SEQRES 20 A 540 ASP GLY ASN SER HIS GLN ALA PHE VAL ARG GLY ASN GLY SEQRES 21 A 540 GLU VAL ILE VAL SER ALA GLY THR ILE GLY THR PRO GLN SEQRES 22 A 540 LEU LEU LEU LEU SER GLY VAL GLY PRO GLU SER TYR LEU SEQRES 23 A 540 SER SER LEU ASN ILE THR VAL VAL GLN PRO ASN PRO TYR SEQRES 24 A 540 VAL GLY GLN PHE VAL TYR ASP ASN PRO ARG ASN PHE ILE SEQRES 25 A 540 ASN ILE LEU PRO PRO ASN PRO ILE GLU ALA SER VAL VAL SEQRES 26 A 540 THR VAL LEU GLY ILE ARG SER ASP TYR TYR GLN VAL SER SEQRES 27 A 540 ALA SER SER LEU PRO PHE SER THR PRO PRO PHE SER LEU SEQRES 28 A 540 PHE PRO THR THR SER TYR PRO LEU PRO ASN SER THR PHE SEQRES 29 A 540 ALA HIS ILE VAL SER GLN VAL PRO GLY PRO LEU SER HIS SEQRES 30 A 540 GLY SER VAL THR LEU ASN SER SER SER ASP VAL ARG ILE SEQRES 31 A 540 ALA PRO ASN ILE LYS PHE ASN TYR TYR SER ASN SER THR SEQRES 32 A 540 ASP LEU ALA ASN CYS VAL SER GLY MET LYS LYS LEU GLY SEQRES 33 A 540 ASP LEU LEU ARG THR LYS ALA LEU GLU PRO TYR LYS ALA SEQRES 34 A 540 ARG ASP VAL LEU GLY ILE ASP GLY PHE ASN TYR LEU GLY SEQRES 35 A 540 VAL PRO LEU PRO GLU ASN GLN THR ASP ASP ALA SER PHE SEQRES 36 A 540 GLU THR PHE CYS LEU ASP ASN VAL ALA SER TYR TRP HIS SEQRES 37 A 540 TYR HIS GLY GLY SER LEU VAL GLY LYS VAL LEU ASP ASP SEQRES 38 A 540 SER PHE ARG VAL MET GLY ILE LYS ALA LEU ARG VAL VAL SEQRES 39 A 540 ASP ALA SER THR PHE PRO TYR GLU PRO ASN SER HIS PRO SEQRES 40 A 540 GLN GLY PHE TYR LEU MET LEU GLY ARG TYR VAL GLY LEU SEQRES 41 A 540 GLN ILE LEU GLN GLU ARG SER ILE ARG LEU GLU ALA ILE SEQRES 42 A 540 HIS ASN ILE GLN GLU SER MET HET NAG A 601 14 HET NAG A 602 14 HET NAG A 603 14 HET NAG A 604 14 HET NAG A 605 14 HET NAG A 606 14 HET FQ6 A 607 12 HET FAD A 608 53 HET PEG A 609 7 HET PO4 A 610 5 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FQ6 4H-1,3-BENZODIOXINE-6-CARBALDEHYDE HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM PEG DI(HYDROXYETHYL)ETHER HETNAM PO4 PHOSPHATE ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN FQ6 4H-BENZO[D][1,3]DIOXINE-6-CARBALDEHYDE FORMUL 2 NAG 6(C8 H15 N O6) FORMUL 8 FQ6 C9 H8 O3 FORMUL 9 FAD C27 H33 N9 O15 P2 FORMUL 10 PEG C4 H10 O3 FORMUL 11 PO4 O4 P 3- FORMUL 12 HOH *296(H2 O) HELIX 1 AA1 PHE A 9 LYS A 13 5 5 HELIX 2 AA2 ASP A 20 GLU A 24 5 5 HELIX 3 AA3 SER A 37 SER A 46 1 10 HELIX 4 AA4 ILE A 59 ASP A 70 5 12 HELIX 5 AA5 GLY A 71 GLN A 78 1 8 HELIX 6 AA6 GLY A 104 ILE A 109 5 6 HELIX 7 AA7 SER A 120 GLY A 126 1 7 HELIX 8 AA8 ASP A 130 VAL A 146 1 17 HELIX 9 AA9 GLN A 152 ALA A 165 1 14 HELIX 10 AB1 ALA A 196 GLY A 204 5 9 HELIX 11 AB2 ALA A 258 SER A 270 1 13 HELIX 12 AB3 PRO A 274 LEU A 281 1 8 HELIX 13 AB4 ASN A 393 ARG A 412 1 20 HELIX 14 AB5 THR A 413 LYS A 420 5 8 HELIX 15 AB6 GLY A 426 PHE A 430 5 5 HELIX 16 AB7 ASP A 443 VAL A 455 1 13 HELIX 17 AB8 ASP A 487 PHE A 491 5 5 HELIX 18 AB9 PRO A 499 SER A 519 1 21 SHEET 1 AA1 7 VAL A 15 ASN A 17 0 SHEET 2 AA1 7 LEU A 209 VAL A 213 1 O VAL A 211 N TYR A 16 SHEET 3 AA1 7 VAL A 51 GLU A 55 1 N LEU A 53 O ALA A 212 SHEET 4 AA1 7 GLY A 25 ILE A 32 1 N VAL A 31 O LEU A 52 SHEET 5 AA1 7 SER A 243 VAL A 256 1 O PHE A 247 N GLY A 25 SHEET 6 AA1 7 ALA A 231 THR A 237 -1 N TYR A 236 O HIS A 244 SHEET 7 AA1 7 SER A 216 PHE A 222 -1 N LEU A 221 O ILE A 232 SHEET 1 AA2 6 VAL A 15 ASN A 17 0 SHEET 2 AA2 6 LEU A 209 VAL A 213 1 O VAL A 211 N TYR A 16 SHEET 3 AA2 6 VAL A 51 GLU A 55 1 N LEU A 53 O ALA A 212 SHEET 4 AA2 6 GLY A 25 ILE A 32 1 N VAL A 31 O LEU A 52 SHEET 5 AA2 6 SER A 243 VAL A 256 1 O PHE A 247 N GLY A 25 SHEET 6 AA2 6 LEU A 483 VAL A 485 1 O ARG A 484 N VAL A 256 SHEET 1 AA3 2 VAL A 86 VAL A 90 0 SHEET 2 AA3 2 ASP A 96 ALA A 100 -1 O ARG A 99 N GLU A 87 SHEET 1 AA4 2 VAL A 113 TYR A 114 0 SHEET 2 AA4 2 GLY A 185 SER A 186 -1 O GLY A 185 N TYR A 114 SHEET 1 AA5 7 ASP A 170 PHE A 173 0 SHEET 2 AA5 7 GLY A 180 LEU A 183 1 O THR A 181 N ASN A 171 SHEET 3 AA5 7 VAL A 319 ARG A 323 -1 O ILE A 322 N GLY A 180 SHEET 4 AA5 7 TYR A 326 SER A 333 -1 O GLN A 328 N GLY A 321 SHEET 5 AA5 7 PHE A 356 GLN A 362 -1 O HIS A 358 N ALA A 331 SHEET 6 AA5 7 PRO A 300 ILE A 306 -1 N ILE A 304 O ILE A 359 SHEET 7 AA5 7 TYR A 432 LEU A 433 -1 O LEU A 433 N ASN A 305 SHEET 1 AA6 7 ASP A 170 PHE A 173 0 SHEET 2 AA6 7 GLY A 180 LEU A 183 1 O THR A 181 N ASN A 171 SHEET 3 AA6 7 VAL A 319 ARG A 323 -1 O ILE A 322 N GLY A 180 SHEET 4 AA6 7 TYR A 326 SER A 333 -1 O GLN A 328 N GLY A 321 SHEET 5 AA6 7 PHE A 356 GLN A 362 -1 O HIS A 358 N ALA A 331 SHEET 6 AA6 7 PRO A 300 ILE A 306 -1 N ILE A 304 O ILE A 359 SHEET 7 AA6 7 ALA A 456 SER A 457 -1 O ALA A 456 N ARG A 301 SHEET 1 AA7 2 VAL A 272 GLY A 273 0 SHEET 2 AA7 2 GLN A 287 PRO A 288 1 O GLN A 287 N GLY A 273 SHEET 1 AA8 4 ASN A 385 LYS A 387 0 SHEET 2 AA8 4 GLY A 370 THR A 373 -1 N THR A 373 O ASN A 385 SHEET 3 AA8 4 GLN A 294 TYR A 297 -1 N VAL A 296 O GLY A 370 SHEET 4 AA8 4 HIS A 462 GLY A 463 -1 O HIS A 462 N TYR A 297 SSBOND 1 CYS A 400 CYS A 451 1555 1555 2.10 LINK ND2 ASN A 17 C1 NAG A 601 1555 1555 1.44 LINK ND2 ASN A 118 C1 NAG A 605 1555 1555 1.47 LINK ND2 ASN A 135 C1 NAG A 602 1555 1555 1.43 LINK ND2 ASN A 282 C1 NAG A 603 1555 1555 1.45 LINK ND2 ASN A 375 C1 NAG A 604 1555 1555 1.43 LINK ND2 ASN A 393 C1 NAG A 606 1555 1555 1.43 CISPEP 1 LEU A 168 PRO A 169 0 2.96 CISPEP 2 GLY A 365 PRO A 366 0 -6.94 CRYST1 49.648 91.713 129.724 90.00 90.00 90.00 P 21 21 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 0.020142 0.000000 0.000000 0.00000 SCALE2 0.000000 0.010904 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007709 0.00000 CONECT 151 3958 CONECT 906 4014 CONECT 1047 3972 CONECT 2116 3986 CONECT 2840 4000 CONECT 2986 4028 CONECT 3034 3412 CONECT 3412 3034 CONECT 3958 151 3959 3969 CONECT 3959 3958 3960 3966 CONECT 3960 3959 3961 3967 CONECT 3961 3960 3962 3968 CONECT 3962 3961 3963 3969 CONECT 3963 3962 3970 CONECT 3964 3965 3966 3971 CONECT 3965 3964 CONECT 3966 3959 3964 CONECT 3967 3960 CONECT 3968 3961 CONECT 3969 3958 3962 CONECT 3970 3963 CONECT 3971 3964 CONECT 3972 1047 3973 3983 CONECT 3973 3972 3974 3980 CONECT 3974 3973 3975 3981 CONECT 3975 3974 3976 3982 CONECT 3976 3975 3977 3983 CONECT 3977 3976 3984 CONECT 3978 3979 3980 3985 CONECT 3979 3978 CONECT 3980 3973 3978 CONECT 3981 3974 CONECT 3982 3975 CONECT 3983 3972 3976 CONECT 3984 3977 CONECT 3985 3978 CONECT 3986 2116 3987 3997 CONECT 3987 3986 3988 3994 CONECT 3988 3987 3989 3995 CONECT 3989 3988 3990 3996 CONECT 3990 3989 3991 3997 CONECT 3991 3990 3998 CONECT 3992 3993 3994 3999 CONECT 3993 3992 CONECT 3994 3987 3992 CONECT 3995 3988 CONECT 3996 3989 CONECT 3997 3986 3990 CONECT 3998 3991 CONECT 3999 3992 CONECT 4000 2840 4001 4011 CONECT 4001 4000 4002 4008 CONECT 4002 4001 4003 4009 CONECT 4003 4002 4004 4010 CONECT 4004 4003 4005 4011 CONECT 4005 4004 4012 CONECT 4006 4007 4008 4013 CONECT 4007 4006 CONECT 4008 4001 4006 CONECT 4009 4002 CONECT 4010 4003 CONECT 4011 4000 4004 CONECT 4012 4005 CONECT 4013 4006 CONECT 4014 906 4015 4025 CONECT 4015 4014 4016 4022 CONECT 4016 4015 4017 4023 CONECT 4017 4016 4018 4024 CONECT 4018 4017 4019 4025 CONECT 4019 4018 4026 CONECT 4020 4021 4022 4027 CONECT 4021 4020 CONECT 4022 4015 4020 CONECT 4023 4016 CONECT 4024 4017 CONECT 4025 4014 4018 CONECT 4026 4019 CONECT 4027 4020 CONECT 4028 2986 4029 4039 CONECT 4029 4028 4030 4036 CONECT 4030 4029 4031 4037 CONECT 4031 4030 4032 4038 CONECT 4032 4031 4033 4039 CONECT 4033 4032 4040 CONECT 4034 4035 4036 4041 CONECT 4035 4034 CONECT 4036 4029 4034 CONECT 4037 4030 CONECT 4038 4031 CONECT 4039 4028 4032 CONECT 4040 4033 CONECT 4041 4034 CONECT 4042 4043 4047 CONECT 4043 4042 4044 4048 CONECT 4044 4043 4045 4052 CONECT 4045 4044 4046 CONECT 4046 4045 4047 CONECT 4047 4042 4046 4050 CONECT 4048 4043 4051 CONECT 4049 4051 4052 CONECT 4050 4047 4053 CONECT 4051 4048 4049 CONECT 4052 4044 4049 CONECT 4053 4050 CONECT 4054 4055 4056 4057 4106 CONECT 4055 4054 CONECT 4056 4054 CONECT 4057 4054 4058 CONECT 4058 4057 4059 CONECT 4059 4058 4060 4061 CONECT 4060 4059 4065 CONECT 4061 4059 4062 4063 CONECT 4062 4061 CONECT 4063 4061 4064 4065 CONECT 4064 4063 CONECT 4065 4060 4063 4066 CONECT 4066 4065 4067 4075 CONECT 4067 4066 4068 CONECT 4068 4067 4069 CONECT 4069 4068 4070 4075 CONECT 4070 4069 4071 4072 CONECT 4071 4070 CONECT 4072 4070 4073 CONECT 4073 4072 4074 CONECT 4074 4073 4075 CONECT 4075 4066 4069 4074 CONECT 4076 4077 4093 CONECT 4077 4076 4078 4079 CONECT 4078 4077 CONECT 4079 4077 4080 CONECT 4080 4079 4081 4082 CONECT 4081 4080 CONECT 4082 4080 4083 4093 CONECT 4083 4082 4084 CONECT 4084 4083 4085 4091 CONECT 4085 4084 4086 CONECT 4086 4085 4087 4088 CONECT 4087 4086 CONECT 4088 4086 4089 4090 CONECT 4089 4088 CONECT 4090 4088 4091 CONECT 4091 4084 4090 4092 CONECT 4092 4091 4093 4094 CONECT 4093 4076 4082 4092 CONECT 4094 4092 4095 CONECT 4095 4094 4096 4097 CONECT 4096 4095 CONECT 4097 4095 4098 4099 CONECT 4098 4097 CONECT 4099 4097 4100 4101 CONECT 4100 4099 CONECT 4101 4099 4102 CONECT 4102 4101 4103 CONECT 4103 4102 4104 4105 4106 CONECT 4104 4103 CONECT 4105 4103 CONECT 4106 4054 4103 CONECT 4107 4108 4109 CONECT 4108 4107 CONECT 4109 4107 4110 CONECT 4110 4109 4111 CONECT 4111 4110 4112 CONECT 4112 4111 4113 CONECT 4113 4112 CONECT 4114 4115 4116 4117 4118 CONECT 4115 4114 CONECT 4116 4114 CONECT 4117 4114 CONECT 4118 4114 MASTER 353 0 10 18 37 0 0 6 4405 1 169 42 END