HEADER LYASE 17-OCT-15 5EB4 TITLE THE CRYSTAL STRUCTURE OF ALMOND HNL, PAHNL5 V317A, EXPRESSED IN TITLE 2 ASPERGILLUS NIGER CAVEAT 5EB4 NAG A 605 HAS WRONG CHIRALITY AT ATOM C1 NAG B 607 HAS WRONG CAVEAT 2 5EB4 CHIRALITY AT ATOM C1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: HNL ISOENZYME 5; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: UNP RESIDUES 28-559; COMPND 5 SYNONYM: HYDROXYNITRILE LYASE; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PRUNUS DULCIS; SOURCE 3 ORGANISM_COMMON: ALMOND; SOURCE 4 ORGANISM_TAXID: 3755; SOURCE 5 GENE: HNL5; SOURCE 6 EXPRESSION_SYSTEM: ASPERGILLUS NIGER; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 5061 KEYWDS HYDROXYNITRILE LYASE, PRUNUS AMYGDALUS, ASPERGILLUS NIGER, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR T.PAVKOV-KELLER,G.STEINKELLNER,K.GRUBER REVDAT 5 10-JAN-24 5EB4 1 HETSYN REVDAT 4 29-JUL-20 5EB4 1 COMPND REMARK HETNAM LINK REVDAT 4 2 1 SITE ATOM REVDAT 3 05-OCT-16 5EB4 1 JRNL REVDAT 2 27-APR-16 5EB4 1 JRNL REVDAT 1 20-APR-16 5EB4 0 JRNL AUTH T.PAVKOV-KELLER,J.BAKHUIS,G.STEINKELLNER,F.JOLINK,E.KEIJMEL, JRNL AUTH 2 R.BIRNER-GRUENBERGER,K.GRUBER JRNL TITL STRUCTURES OF ALMOND HYDROXYNITRILE LYASE ISOENZYME 5 JRNL TITL 2 PROVIDE A RATIONALE FOR THE LACK OF OXIDOREDUCTASE ACTIVITY JRNL TITL 3 IN FLAVIN DEPENDENT HNLS. JRNL REF J.BIOTECHNOL. V. 235 24 2016 JRNL REFN ISSN 0168-1656 JRNL PMID 27067080 JRNL DOI 10.1016/J.JBIOTEC.2016.04.013 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0131 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.09 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 91.7 REMARK 3 NUMBER OF REFLECTIONS : 47293 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) : 0.190 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.247 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 2491 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) : 2.30 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.36 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3377 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 89.52 REMARK 3 BIN R VALUE (WORKING SET) : 0.2660 REMARK 3 BIN FREE R VALUE SET COUNT : 178 REMARK 3 BIN FREE R VALUE : 0.2970 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7857 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 330 REMARK 3 SOLVENT ATOMS : 464 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.21000 REMARK 3 B22 (A**2) : -2.16000 REMARK 3 B33 (A**2) : 3.12000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 1.69000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.373 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.255 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.212 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 9.043 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.917 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 8427 ; 0.013 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 11535 ; 1.708 ; 2.004 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 1025 ; 6.970 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 366 ;36.411 ;24.754 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1217 ;14.681 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;16.937 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1327 ; 0.111 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 6467 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 4106 ; 1.638 ; 2.383 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5129 ; 2.727 ; 3.566 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 4321 ; 2.376 ; 2.647 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 12836 ; 5.735 ;20.389 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 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 USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 5EB4 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-OCT-15. REMARK 100 THE DEPOSITION ID IS D_1000214601. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-MAY-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 - 7.8 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SLS REMARK 200 BEAMLINE : X06SA REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49502 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.300 REMARK 200 RESOLUTION RANGE LOW (A) : 49.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 91.4 REMARK 200 DATA REDUNDANCY : 5.300 REMARK 200 R MERGE (I) : 0.18800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.30 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.35 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : 0.56600 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.500 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: 1JU2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.99 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.67 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: THE INITIAL PROTEIN CONCENTRATION WAS REMARK 280 28 MG/ML (10MM L-MALIC ACID, MES, TRIS PH 7). DIFFERENT CRYSTAL REMARK 280 FORMS WERE OBTAINED UNDER CRYSTALLIZATION CONDITIONS VARYING - REMARK 280 PEG 4K, ISOPROPANOL AND 10MM HEPES PH 7-7.8 WITH PROTEIN REMARK 280 CONCENTRATION 19-28 MG/ML. MOST OF THE CRYSTALS THAT APPEARED REMARK 280 WITHIN 2 WEEKS HAD VISUAL GROW DEFECTS. IN ONE OF THE DROPS THE REMARK 280 STACK OF THIN PLATES APPEARED AFTER 1 MONTH AND ONE COMPLETE REMARK 280 DATASET WAS COLLECTED., VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 46.15000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 APPLY THE FOLLOWING TO CHAINS: A, C 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B, D, E 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 LEU A 1 REMARK 465 ASN A 225 REMARK 465 THR A 226 REMARK 465 SER A 227 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 465 LEU B 1 REMARK 465 SER B 224 REMARK 465 ASN B 225 REMARK 465 THR B 226 REMARK 465 SER B 227 REMARK 465 GLU B 439 REMARK 465 ASN B 440 REMARK 465 GLN B 441 REMARK 465 THR B 442 REMARK 465 ASP B 443 REMARK 465 ILE B 520 REMARK 465 ARG B 521 REMARK 465 LEU B 522 REMARK 465 GLU B 523 REMARK 465 ALA B 524 REMARK 465 ILE B 525 REMARK 465 HIS B 526 REMARK 465 ASN B 527 REMARK 465 ILE B 528 REMARK 465 GLN B 529 REMARK 465 GLU B 530 REMARK 465 SER B 531 REMARK 465 MET B 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 O HOH B 911 O HOH B 923 1.99 REMARK 500 O HOH B 769 O HOH B 897 2.04 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 LEU A 331 CA - CB - CG ANGL. DEV. = 14.4 DEGREES REMARK 500 LEU B 331 CA - CB - CG ANGL. DEV. = 15.0 DEGREES REMARK 500 ASP B 472 CB - CG - OD1 ANGL. DEV. = 5.5 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 342 -0.99 72.36 REMARK 500 ASN A 440 -30.30 64.28 REMARK 500 HIS A 460 35.80 -95.56 REMARK 500 SER A 465 58.84 -146.33 REMARK 500 ASP A 473 -7.83 -59.07 REMARK 500 PHE A 475 10.13 81.80 REMARK 500 ASP A 487 -159.98 -178.24 REMARK 500 ASN A 496 -173.17 178.38 REMARK 500 ASN B 110 -169.14 -78.55 REMARK 500 PHE B 295 61.32 61.86 REMARK 500 SER B 342 -8.32 74.96 REMARK 500 TYR B 390 130.44 -37.57 REMARK 500 HIS B 460 39.98 -95.31 REMARK 500 SER B 465 53.40 -151.15 REMARK 500 ASP B 487 -160.49 -177.23 REMARK 500 ASN B 496 -175.64 -179.26 REMARK 500 REMARK 500 REMARK: NULL DBREF 5EB4 A 1 532 UNP Q7XJE8 Q7XJE8_PRUDU 28 559 DBREF 5EB4 B 1 532 UNP Q7XJE8 Q7XJE8_PRUDU 28 559 SEQADV 5EB4 ALA A 317 UNP Q7XJE8 VAL 344 ENGINEERED MUTATION SEQADV 5EB4 VAL A 360 UNP Q7XJE8 UNK 387 CONFLICT SEQADV 5EB4 ASN A 496 UNP Q7XJE8 UNK 523 CONFLICT SEQADV 5EB4 ALA B 317 UNP Q7XJE8 VAL 344 ENGINEERED MUTATION SEQADV 5EB4 VAL B 360 UNP Q7XJE8 UNK 387 CONFLICT SEQADV 5EB4 ASN B 496 UNP Q7XJE8 UNK 523 CONFLICT SEQRES 1 A 532 LEU ALA ASN THR SER ALA HIS ASP PHE SER TYR LEU LYS SEQRES 2 A 532 PHE VAL TYR ASN ALA THR ASP THR SER SER GLU GLY SER SEQRES 3 A 532 TYR ASP TYR ILE VAL ILE GLY GLY GLY THR SER GLY CYS SEQRES 4 A 532 PRO LEU ALA ALA THR LEU SER GLU LYS TYR LYS VAL LEU SEQRES 5 A 532 LEU LEU GLU ARG GLY THR ILE ALA THR GLU TYR PRO ASN SEQRES 6 A 532 THR LEU THR ALA ASP GLY PHE ALA TYR ASN LEU GLN GLN SEQRES 7 A 532 GLN ASP ASP GLY LYS THR PRO VAL GLU ARG PHE VAL SER SEQRES 8 A 532 GLU ASP GLY ILE ASP ASN VAL ARG ALA ARG ILE LEU GLY SEQRES 9 A 532 GLY THR THR ILE ILE ASN ALA GLY VAL TYR ALA ARG ALA SEQRES 10 A 532 ASN ILE SER PHE TYR SER GLN THR GLY ILE GLU TRP ASP SEQRES 11 A 532 LEU ASP LEU VAL ASN LYS THR TYR GLU TRP VAL GLU ASP SEQRES 12 A 532 ALA ILE VAL VAL LYS PRO ASN ASN GLN SER TRP GLN SER SEQRES 13 A 532 VAL ILE GLY GLU GLY PHE LEU GLU ALA GLY ILE LEU PRO SEQRES 14 A 532 ASP ASN GLY PHE SER LEU ASP HIS GLU ALA GLY THR ARG SEQRES 15 A 532 LEU THR GLY SER THR PHE ASP ASN ASN GLY THR ARG HIS SEQRES 16 A 532 ALA ALA ASP GLU LEU LEU ASN LYS GLY ASP PRO ASN ASN SEQRES 17 A 532 LEU LEU VAL ALA VAL GLN ALA SER VAL GLU LYS ILE LEU SEQRES 18 A 532 PHE SER SER ASN THR SER ASN LEU SER ALA ILE GLY VAL SEQRES 19 A 532 ILE TYR THR ASP SER ASP GLY ASN SER HIS GLN ALA PHE SEQRES 20 A 532 VAL ARG GLY ASN GLY GLU VAL ILE VAL SER ALA GLY THR SEQRES 21 A 532 ILE GLY THR PRO GLN LEU LEU LEU LEU SER GLY VAL GLY SEQRES 22 A 532 PRO GLU SER TYR LEU SER SER LEU ASN ILE THR VAL VAL SEQRES 23 A 532 GLN PRO ASN PRO TYR VAL GLY GLN PHE VAL TYR ASP ASN SEQRES 24 A 532 PRO ARG ASN PHE ILE ASN ILE LEU PRO PRO ASN PRO ILE SEQRES 25 A 532 GLU ALA SER VAL ALA THR VAL LEU GLY ILE ARG SER ASP SEQRES 26 A 532 TYR TYR GLN VAL SER LEU SER SER LEU PRO PHE SER THR SEQRES 27 A 532 PRO PRO PHE SER LEU PHE PRO THR THR SER TYR PRO LEU SEQRES 28 A 532 PRO ASN SER THR PHE ALA HIS ILE VAL SER GLN VAL PRO SEQRES 29 A 532 GLY PRO LEU SER HIS GLY SER VAL THR LEU ASN SER SER SEQRES 30 A 532 SER ASP VAL ARG ILE ALA PRO ASN ILE LYS PHE ASN TYR SEQRES 31 A 532 TYR SER ASN SER THR ASP LEU ALA ASN CYS VAL SER GLY SEQRES 32 A 532 MET LYS LYS LEU GLY ASP LEU LEU ARG THR LYS ALA LEU SEQRES 33 A 532 GLU PRO TYR LYS ALA ARG ASP VAL LEU GLY ILE ASP GLY SEQRES 34 A 532 PHE ASN TYR LEU GLY VAL PRO LEU PRO GLU ASN GLN THR SEQRES 35 A 532 ASP ASP ALA SER PHE GLU THR PHE CYS LEU ASP ASN VAL SEQRES 36 A 532 ALA SER TYR TRP HIS TYR HIS GLY GLY SER LEU VAL GLY SEQRES 37 A 532 LYS VAL LEU ASP ASP SER PHE ARG VAL MET GLY ILE LYS SEQRES 38 A 532 ALA LEU ARG VAL VAL ASP ALA SER THR PHE PRO TYR GLU SEQRES 39 A 532 PRO ASN SER HIS PRO GLN GLY PHE TYR LEU MET LEU GLY SEQRES 40 A 532 ARG TYR VAL GLY LEU GLN ILE LEU GLN GLU ARG SER ILE SEQRES 41 A 532 ARG LEU GLU ALA ILE HIS ASN ILE GLN GLU SER MET SEQRES 1 B 532 LEU ALA ASN THR SER ALA HIS ASP PHE SER TYR LEU LYS SEQRES 2 B 532 PHE VAL TYR ASN ALA THR ASP THR SER SER GLU GLY SER SEQRES 3 B 532 TYR ASP TYR ILE VAL ILE GLY GLY GLY THR SER GLY CYS SEQRES 4 B 532 PRO LEU ALA ALA THR LEU SER GLU LYS TYR LYS VAL LEU SEQRES 5 B 532 LEU LEU GLU ARG GLY THR ILE ALA THR GLU TYR PRO ASN SEQRES 6 B 532 THR LEU THR ALA ASP GLY PHE ALA TYR ASN LEU GLN GLN SEQRES 7 B 532 GLN ASP ASP GLY LYS THR PRO VAL GLU ARG PHE VAL SER SEQRES 8 B 532 GLU ASP GLY ILE ASP ASN VAL ARG ALA ARG ILE LEU GLY SEQRES 9 B 532 GLY THR THR ILE ILE ASN ALA GLY VAL TYR ALA ARG ALA SEQRES 10 B 532 ASN ILE SER PHE TYR SER GLN THR GLY ILE GLU TRP ASP SEQRES 11 B 532 LEU ASP LEU VAL ASN LYS THR TYR GLU TRP VAL GLU ASP SEQRES 12 B 532 ALA ILE VAL VAL LYS PRO ASN ASN GLN SER TRP GLN SER SEQRES 13 B 532 VAL ILE GLY GLU GLY PHE LEU GLU ALA GLY ILE LEU PRO SEQRES 14 B 532 ASP ASN GLY PHE SER LEU ASP HIS GLU ALA GLY THR ARG SEQRES 15 B 532 LEU THR GLY SER THR PHE ASP ASN ASN GLY THR ARG HIS SEQRES 16 B 532 ALA ALA ASP GLU LEU LEU ASN LYS GLY ASP PRO ASN ASN SEQRES 17 B 532 LEU LEU VAL ALA VAL GLN ALA SER VAL GLU LYS ILE LEU SEQRES 18 B 532 PHE SER SER ASN THR SER ASN LEU SER ALA ILE GLY VAL SEQRES 19 B 532 ILE TYR THR ASP SER ASP GLY ASN SER HIS GLN ALA PHE SEQRES 20 B 532 VAL ARG GLY ASN GLY GLU VAL ILE VAL SER ALA GLY THR SEQRES 21 B 532 ILE GLY THR PRO GLN LEU LEU LEU LEU SER GLY VAL GLY SEQRES 22 B 532 PRO GLU SER TYR LEU SER SER LEU ASN ILE THR VAL VAL SEQRES 23 B 532 GLN PRO ASN PRO TYR VAL GLY GLN PHE VAL TYR ASP ASN SEQRES 24 B 532 PRO ARG ASN PHE ILE ASN ILE LEU PRO PRO ASN PRO ILE SEQRES 25 B 532 GLU ALA SER VAL ALA THR VAL LEU GLY ILE ARG SER ASP SEQRES 26 B 532 TYR TYR GLN VAL SER LEU SER SER LEU PRO PHE SER THR SEQRES 27 B 532 PRO PRO PHE SER LEU PHE PRO THR THR SER TYR PRO LEU SEQRES 28 B 532 PRO ASN SER THR PHE ALA HIS ILE VAL SER GLN VAL PRO SEQRES 29 B 532 GLY PRO LEU SER HIS GLY SER VAL THR LEU ASN SER SER SEQRES 30 B 532 SER ASP VAL ARG ILE ALA PRO ASN ILE LYS PHE ASN TYR SEQRES 31 B 532 TYR SER ASN SER THR ASP LEU ALA ASN CYS VAL SER GLY SEQRES 32 B 532 MET LYS LYS LEU GLY ASP LEU LEU ARG THR LYS ALA LEU SEQRES 33 B 532 GLU PRO TYR LYS ALA ARG ASP VAL LEU GLY ILE ASP GLY SEQRES 34 B 532 PHE ASN TYR LEU GLY VAL PRO LEU PRO GLU ASN GLN THR SEQRES 35 B 532 ASP ASP ALA SER PHE GLU THR PHE CYS LEU ASP ASN VAL SEQRES 36 B 532 ALA SER TYR TRP HIS TYR HIS GLY GLY SER LEU VAL GLY SEQRES 37 B 532 LYS VAL LEU ASP ASP SER PHE ARG VAL MET GLY ILE LYS SEQRES 38 B 532 ALA LEU ARG VAL VAL ASP ALA SER THR PHE PRO TYR GLU SEQRES 39 B 532 PRO ASN SER HIS PRO GLN GLY PHE TYR LEU MET LEU GLY SEQRES 40 B 532 ARG TYR VAL GLY LEU GLN ILE LEU GLN GLU ARG SER ILE SEQRES 41 B 532 ARG LEU GLU ALA ILE HIS ASN ILE GLN GLU SER MET HET NAG C 1 14 HET NAG C 2 14 HET NAG D 1 14 HET NAG D 2 14 HET NAG E 1 14 HET NAG E 2 14 HET NAG A 601 14 HET NAG A 604 14 HET NAG A 605 14 HET NAG A 606 14 HET NAG A 607 14 HET FAD A 608 53 HET NAG B 603 14 HET NAG B 606 14 HET NAG B 607 14 HET NAG B 608 14 HET NAG B 609 14 HET FAD B 610 53 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE 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 FORMUL 3 NAG 16(C8 H15 N O6) FORMUL 11 FAD 2(C27 H33 N9 O15 P2) FORMUL 18 HOH *464(H2 O) HELIX 1 AA1 PHE A 9 LYS A 13 5 5 HELIX 2 AA2 THR A 19 THR A 21 5 3 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 ILE A 119 GLY A 126 1 8 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 LEU A 416 LYS A 420 5 5 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 HELIX 19 AC1 PHE B 9 LYS B 13 5 5 HELIX 20 AC2 THR B 19 THR B 21 5 3 HELIX 21 AC3 SER B 37 SER B 46 1 10 HELIX 22 AC4 ILE B 59 ASP B 70 5 12 HELIX 23 AC5 GLY B 71 GLN B 78 1 8 HELIX 24 AC6 GLY B 104 ILE B 109 5 6 HELIX 25 AC7 ILE B 119 GLY B 126 1 8 HELIX 26 AC8 ASP B 130 VAL B 146 1 17 HELIX 27 AC9 GLN B 152 ALA B 165 1 14 HELIX 28 AD1 ALA B 196 GLY B 204 5 9 HELIX 29 AD2 ALA B 258 SER B 270 1 13 HELIX 30 AD3 PRO B 274 LEU B 281 1 8 HELIX 31 AD4 ASN B 393 ARG B 412 1 20 HELIX 32 AD5 LEU B 416 LYS B 420 5 5 HELIX 33 AD6 GLY B 426 PHE B 430 5 5 HELIX 34 AD7 ALA B 445 ASN B 454 1 10 HELIX 35 AD8 ASP B 487 PHE B 491 5 5 HELIX 36 AD9 PRO B 499 ARG B 518 1 20 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 LEU A 54 1 N LEU A 53 O ALA A 212 SHEET 4 AA1 7 GLU A 24 ILE A 32 1 N VAL A 31 O LEU A 52 SHEET 5 AA1 7 SER A 243 VAL A 256 1 O ILE A 255 N ILE A 30 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 LEU A 54 1 N LEU A 53 O ALA A 212 SHEET 4 AA2 6 GLU A 24 ILE A 32 1 N VAL A 31 O LEU A 52 SHEET 5 AA2 6 SER A 243 VAL A 256 1 O ILE A 255 N ILE A 30 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 LEU A 331 SHEET 6 AA5 7 PRO A 300 LEU A 307 -1 N ASN A 302 O SER A 361 SHEET 7 AA5 7 ASN A 431 LEU A 433 -1 O ASN A 431 N LEU A 307 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 LEU A 331 SHEET 6 AA6 7 PRO A 300 LEU A 307 -1 N ASN A 302 O SER A 361 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 SHEET 1 AA9 7 VAL B 15 ASN B 17 0 SHEET 2 AA9 7 LEU B 209 VAL B 213 1 O VAL B 213 N TYR B 16 SHEET 3 AA9 7 VAL B 51 LEU B 54 1 N LEU B 53 O ALA B 212 SHEET 4 AA9 7 GLU B 24 ILE B 32 1 N VAL B 31 O LEU B 54 SHEET 5 AA9 7 SER B 243 VAL B 256 1 O ILE B 255 N ILE B 32 SHEET 6 AA9 7 ALA B 231 THR B 237 -1 N VAL B 234 O ALA B 246 SHEET 7 AA9 7 SER B 216 PHE B 222 -1 N LEU B 221 O ILE B 232 SHEET 1 AB1 6 VAL B 15 ASN B 17 0 SHEET 2 AB1 6 LEU B 209 VAL B 213 1 O VAL B 213 N TYR B 16 SHEET 3 AB1 6 VAL B 51 LEU B 54 1 N LEU B 53 O ALA B 212 SHEET 4 AB1 6 GLU B 24 ILE B 32 1 N VAL B 31 O LEU B 54 SHEET 5 AB1 6 SER B 243 VAL B 256 1 O ILE B 255 N ILE B 32 SHEET 6 AB1 6 LEU B 483 VAL B 485 1 O ARG B 484 N VAL B 256 SHEET 1 AB2 2 VAL B 86 VAL B 90 0 SHEET 2 AB2 2 ASP B 96 ALA B 100 -1 O ARG B 99 N GLU B 87 SHEET 1 AB3 2 VAL B 113 TYR B 114 0 SHEET 2 AB3 2 GLY B 185 SER B 186 -1 O GLY B 185 N TYR B 114 SHEET 1 AB4 7 ASP B 170 PHE B 173 0 SHEET 2 AB4 7 GLY B 180 LEU B 183 1 O THR B 181 N ASN B 171 SHEET 3 AB4 7 VAL B 319 ILE B 322 -1 O ILE B 322 N GLY B 180 SHEET 4 AB4 7 TYR B 327 SER B 333 -1 O GLN B 328 N GLY B 321 SHEET 5 AB4 7 PHE B 356 GLN B 362 -1 O HIS B 358 N LEU B 331 SHEET 6 AB4 7 PRO B 300 ILE B 306 -1 N ASN B 302 O SER B 361 SHEET 7 AB4 7 ALA B 456 SER B 457 -1 O ALA B 456 N ARG B 301 SHEET 1 AB5 2 VAL B 272 GLY B 273 0 SHEET 2 AB5 2 GLN B 287 PRO B 288 1 O GLN B 287 N GLY B 273 SHEET 1 AB6 4 ASN B 385 LYS B 387 0 SHEET 2 AB6 4 GLY B 370 THR B 373 -1 N THR B 373 O ASN B 385 SHEET 3 AB6 4 GLN B 294 TYR B 297 -1 N VAL B 296 O GLY B 370 SHEET 4 AB6 4 HIS B 462 GLY B 463 -1 O HIS B 462 N TYR B 297 SSBOND 1 CYS A 400 CYS A 451 1555 1555 2.10 SSBOND 2 CYS B 400 CYS B 451 1555 1555 2.08 LINK ND2 ASN A 118 C1 NAG A 606 1555 1555 1.43 LINK ND2 ASN A 135 C1 NAG A 607 1555 1555 1.45 LINK ND2 ASN A 151 C1 NAG A 601 1555 1555 1.46 LINK ND2 ASN A 191 C1 NAG C 1 1555 1555 1.42 LINK ND2 ASN A 375 C1 NAG A 604 1555 1555 1.47 LINK ND2 ASN A 393 C1 NAG A 605 1555 1555 1.43 LINK ND2 ASN B 118 C1 NAG B 608 1555 1555 1.43 LINK ND2 ASN B 135 C1 NAG B 609 1555 1555 1.43 LINK ND2 ASN B 151 C1 NAG B 603 1555 1555 1.44 LINK ND2 ASN B 191 C1 NAG E 1 1555 1555 1.42 LINK ND2 ASN B 353 C1 NAG D 1 1555 1555 1.45 LINK ND2 ASN B 375 C1 NAG B 606 1555 1555 1.45 LINK ND2 ASN B 393 C1 NAG B 607 1555 1555 1.46 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.46 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.46 CISPEP 1 LEU A 168 PRO A 169 0 -1.64 CISPEP 2 GLY A 365 PRO A 366 0 -11.16 CISPEP 3 LEU B 168 PRO B 169 0 4.45 CISPEP 4 GLY B 365 PRO B 366 0 -6.78 CRYST1 68.880 92.300 97.590 90.00 93.73 90.00 P 1 21 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 0.014518 0.000000 0.000947 0.00000 SCALE2 0.000000 0.010834 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010269 0.00000