HEADER OXIDOREDUCTASE 23-SEP-20 7D4E TITLE STRUCTURE OF L-LYSINE OXIDASE PRECURSOR IN COMPLEX WITH L-LYSINE (1.0 TITLE 2 M) COMPND MOL_ID: 1; COMPND 2 MOLECULE: L-LYSINE ALPHA-OXIDASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HYPOCREA RUFA; SOURCE 3 ORGANISM_TAXID: 5547; SOURCE 4 GENE: LYSOX; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: SOLU BL21; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PCOLD IV KEYWDS L-AMINO ACID OXIDASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR M.KITAGAWA,N.ITO,Y.MATSUMOTO,K.INAGAKI,K.IMADA REVDAT 3 29-NOV-23 7D4E 1 REMARK REVDAT 2 24-FEB-21 7D4E 1 JRNL REVDAT 1 10-FEB-21 7D4E 0 JRNL AUTH M.KITAGAWA,N.ITO,Y.MATSUMOTO,M.SAITO,T.TAMURA,H.KUSAKABE, JRNL AUTH 2 K.INAGAKI,K.IMADA JRNL TITL STRUCTURAL BASIS OF ENZYME ACTIVITY REGULATION BY THE JRNL TITL 2 PROPEPTIDE OF L-LYSINE ALPHA-OXIDASE PRECURSOR FROM JRNL TITL 3 TRICHODERMA VIRIDE . JRNL REF J STRUCT BIOL X V. 5 00044 2021 JRNL REFN ESSN 2590-1524 JRNL PMID 33554108 JRNL DOI 10.1016/J.YJSBX.2021.100044 REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.15.2_3472: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 65.03 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 49596 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.160 REMARK 3 FREE R VALUE TEST SET COUNT : 2558 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 65.0250 - 4.8478 0.99 2804 147 0.2022 0.1886 REMARK 3 2 4.8478 - 3.8480 1.00 2684 138 0.1357 0.1592 REMARK 3 3 3.8480 - 3.3616 0.99 2632 143 0.1421 0.1755 REMARK 3 4 3.3616 - 3.0542 0.99 2670 116 0.1617 0.2067 REMARK 3 5 3.0542 - 2.8353 0.99 2633 148 0.1662 0.2287 REMARK 3 6 2.8353 - 2.6682 1.00 2632 126 0.1640 0.2533 REMARK 3 7 2.6682 - 2.5345 1.00 2625 129 0.1639 0.1864 REMARK 3 8 2.5345 - 2.4242 0.99 2628 135 0.1530 0.1941 REMARK 3 9 2.4242 - 2.3309 0.98 2568 146 0.1513 0.2242 REMARK 3 10 2.3309 - 2.2504 0.99 2573 141 0.1578 0.2057 REMARK 3 11 2.2504 - 2.1801 0.99 2620 125 0.1637 0.2455 REMARK 3 12 2.1801 - 2.1177 0.99 2595 134 0.1708 0.2066 REMARK 3 13 2.1177 - 2.0620 0.99 2549 153 0.1707 0.2227 REMARK 3 14 2.0620 - 2.0117 0.99 2587 162 0.1780 0.2566 REMARK 3 15 2.0117 - 1.9659 0.99 2556 149 0.1829 0.2153 REMARK 3 16 1.9659 - 1.9241 0.99 2578 152 0.1942 0.2443 REMARK 3 17 1.9241 - 1.8856 0.98 2544 154 0.2034 0.2348 REMARK 3 18 1.8856 - 1.8500 0.99 2560 160 0.2134 0.3016 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.190 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.010 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 18.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.019 5324 REMARK 3 ANGLE : 1.631 7249 REMARK 3 CHIRALITY : 0.098 763 REMARK 3 PLANARITY : 0.011 938 REMARK 3 DIHEDRAL : 8.721 3942 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7D4E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 24-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1300018723. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 26-OCT-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL41XU REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : DOUBLE-CRYSTAL MONOCHROMATOR REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 49629 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.850 REMARK 200 RESOLUTION RANGE LOW (A) : 76.700 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 4.400 REMARK 200 R MERGE (I) : 0.04800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.89 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.50 REMARK 200 R MERGE FOR SHELL (I) : 0.32200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.000 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: 3X0V REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M TRIS-HCL PH8.0 (-9.0) AND 2.1 M REMARK 280 AMMONIUM DIHYDROGEN PHOSPHATE, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K 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 47.12500 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 47.12500 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 47.44450 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 65.02500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 47.44450 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 65.02500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 47.12500 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 47.44450 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 65.02500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 47.12500 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 47.44450 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 65.02500 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: 8150 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 41810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 940 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 941 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 994 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1002 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1135 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1164 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1186 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 ASP A 2 REMARK 465 ASN A 3 REMARK 465 VAL A 4 REMARK 465 ARG A 33 REMARK 465 LEU A 34 REMARK 465 GLY A 35 REMARK 465 GLU A 36 REMARK 465 VAL A 37 REMARK 465 PRO A 38 REMARK 465 GLY A 39 REMARK 465 ILE A 40 REMARK 465 PRO A 41 REMARK 465 PRO A 42 REMARK 465 PRO A 43 REMARK 465 ARG A 44 REMARK 465 GLU A 45 REMARK 465 GLY A 46 REMARK 465 ARG A 47 REMARK 465 PHE A 48 REMARK 465 LEU A 49 REMARK 465 GLY A 50 REMARK 465 LYS A 68 REMARK 465 PRO A 69 REMARK 465 ALA A 70 REMARK 465 LEU A 71 REMARK 465 LEU A 72 REMARK 465 LYS A 73 REMARK 465 GLU A 74 REMARK 465 ALA A 75 REMARK 465 PRO A 76 REMARK 465 ARG A 77 REMARK 465 ALA A 78 REMARK 465 GLU A 612 REMARK 465 TYR A 613 REMARK 465 GLN A 614 REMARK 465 VAL A 615 REMARK 465 LYS A 616 REMARK 465 ILE A 617 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 NH1 ARG A 387 O HOH A 801 1.81 REMARK 500 NZ LYS A 153 O HOH A 802 1.89 REMARK 500 O HOH A 829 O HOH A 1020 1.91 REMARK 500 O HOH A 802 O HOH A 961 1.91 REMARK 500 O GLY A 253 O HOH A 803 1.92 REMARK 500 OE2 GLU A 491 O HOH A 804 1.95 REMARK 500 O HOH A 934 O HOH A 1173 1.96 REMARK 500 NZ LYS A 460 O HOH A 805 2.00 REMARK 500 O LYS A 135 O HOH A 806 2.01 REMARK 500 ND2 ASN A 182 O HOH A 807 2.02 REMARK 500 OD2 ASP A 241 OG SER A 525 2.02 REMARK 500 O HOH A 1103 O HOH A 1173 2.05 REMARK 500 O HOH A 830 O HOH A 1030 2.06 REMARK 500 O HOH A 878 O HOH A 1175 2.10 REMARK 500 N HIS A 136 O HOH A 808 2.10 REMARK 500 O HOH A 853 O HOH A 1114 2.14 REMARK 500 NE ARG A 387 O HOH A 809 2.15 REMARK 500 O HOH A 974 O HOH A 1167 2.16 REMARK 500 O ASP A 56 O HOH A 810 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 A 823 O HOH A 823 3554 1.88 REMARK 500 OD2 ASP A 133 NZ LYS A 135 3654 2.07 REMARK 500 O HOH A 963 O HOH A 1201 6554 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 ASP A 133 CB ASP A 133 CG -0.236 REMARK 500 LYS A 135 CB LYS A 135 CG -0.174 REMARK 500 LYS A 135 CG LYS A 135 CD -0.224 REMARK 500 GLU A 213 CB GLU A 213 CG -0.124 REMARK 500 VAL A 240 CB VAL A 240 CG1 -0.168 REMARK 500 CYS A 414 CB CYS A 414 SG -0.099 REMARK 500 CYS A 427 CB CYS A 427 SG -0.097 REMARK 500 PRO A 430 CD PRO A 430 N -0.210 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 ASP A 133 CB - CG - OD1 ANGL. DEV. = 12.8 DEGREES REMARK 500 ASP A 133 CB - CG - OD2 ANGL. DEV. = -7.6 DEGREES REMARK 500 LYS A 135 CD - CE - NZ ANGL. DEV. = -50.8 DEGREES REMARK 500 GLU A 213 CA - CB - CG ANGL. DEV. = -18.6 DEGREES REMARK 500 PRO A 296 C - N - CD ANGL. DEV. = -13.5 DEGREES REMARK 500 LEU A 518 CA - CB - CG ANGL. DEV. = -18.3 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 92 53.29 -117.66 REMARK 500 MET A 144 -19.43 -144.65 REMARK 500 ASP A 229 117.40 -169.80 REMARK 500 THR A 274 -149.94 -154.55 REMARK 500 PHE A 293 55.52 -113.29 REMARK 500 THR A 297 33.10 -72.23 REMARK 500 LYS A 298 51.72 -119.04 REMARK 500 LYS A 298 70.48 47.71 REMARK 500 CYS A 414 42.72 -141.43 REMARK 500 CYS A 414 41.80 -140.92 REMARK 500 ARG A 425 -53.92 64.32 REMARK 500 SER A 449 -144.02 58.17 REMARK 500 VAL A 512 -54.22 -137.54 REMARK 500 PHE A 516 163.65 177.46 REMARK 500 ALA A 552 -7.13 90.78 REMARK 500 PRO A 610 -168.63 -72.89 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLU A 80 GLU A 81 148.47 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 A1229 DISTANCE = 5.88 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FAD A 701 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LYS A 702 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3X0V RELATED DB: PDB REMARK 900 THE MATURE FORM REMARK 900 RELATED ID: 7C3H RELATED DB: PDB REMARK 900 THE LIGAND COMPLEX OF THE MATURE FORM REMARK 900 RELATED ID: 7D4C RELATED DB: PDB REMARK 900 LIGAND FREE FORM REMARK 900 RELATED ID: 7D4D RELATED DB: PDB REMARK 900 HIGH LIGAND CONC. DBREF1 7D4E A 1 617 UNP A0A0G4DCU0_HYPRU DBREF2 7D4E A A0A0G4DCU0 1 617 SEQRES 1 A 617 MET ASP ASN VAL ASP PHE ALA GLU SER VAL ARG THR ARG SEQRES 2 A 617 TRP ALA ARG ARG LEU ILE ARG GLU LYS VAL ALA LYS GLU SEQRES 3 A 617 LEU ASN ILE LEU THR GLU ARG LEU GLY GLU VAL PRO GLY SEQRES 4 A 617 ILE PRO PRO PRO ARG GLU GLY ARG PHE LEU GLY GLY GLY SEQRES 5 A 617 TYR SER HIS ASP ASN LEU PRO SER ASP PRO LEU TYR SER SEQRES 6 A 617 SER ILE LYS PRO ALA LEU LEU LYS GLU ALA PRO ARG ALA SEQRES 7 A 617 GLU GLU GLU LEU PRO PRO ARG LYS VAL CYS ILE VAL GLY SEQRES 8 A 617 ALA GLY VAL SER GLY LEU TYR ILE ALA MET ILE LEU ASP SEQRES 9 A 617 ASP LEU LYS ILE PRO ASN LEU THR TYR ASP ILE PHE GLU SEQRES 10 A 617 SER SER SER ARG THR GLY GLY ARG LEU TYR THR HIS HIS SEQRES 11 A 617 PHE THR ASP ALA LYS HIS ASP TYR TYR ASP ILE GLY ALA SEQRES 12 A 617 MET ARG TYR PRO ASP ILE PRO SER MET LYS ARG THR PHE SEQRES 13 A 617 ASN LEU PHE LYS ARG THR GLY MET PRO LEU ILE LYS TYR SEQRES 14 A 617 TYR LEU ASP GLY GLU ASN THR PRO GLN LEU TYR ASN ASN SEQRES 15 A 617 HIS PHE PHE ALA LYS GLY VAL VAL ASP PRO TYR MET VAL SEQRES 16 A 617 SER VAL ALA ASN GLY GLY THR VAL PRO ASP ASP VAL VAL SEQRES 17 A 617 ASP SER VAL GLY GLU LYS LEU GLN GLN ALA PHE GLY TYR SEQRES 18 A 617 TYR LYS GLU LYS LEU ALA GLU ASP PHE ASP LYS GLY PHE SEQRES 19 A 617 ASP GLU LEU MET LEU VAL ASP ASP MET THR THR ARG GLU SEQRES 20 A 617 TYR LEU LYS ARG GLY GLY PRO LYS GLY GLU ALA PRO LYS SEQRES 21 A 617 TYR ASP PHE PHE ALA ILE GLN TRP MET GLU THR GLN ASN SEQRES 22 A 617 THR GLY THR ASN LEU PHE ASP GLN ALA PHE SER GLU SER SEQRES 23 A 617 VAL ILE ASP SER PHE ASP PHE ASP ASN PRO THR LYS PRO SEQRES 24 A 617 GLU TRP TYR CYS ILE GLU GLY GLY THR SER LEU LEU VAL SEQRES 25 A 617 ASP ALA MET LYS GLU THR LEU VAL HIS LYS VAL GLN ASN SEQRES 26 A 617 ASN LYS ARG VAL GLU ALA ILE SER ILE ASP LEU ASP ALA SEQRES 27 A 617 PRO ASP ASP GLY ASN MET SER VAL LYS ILE GLY GLY LYS SEQRES 28 A 617 ASP TYR SER GLY TYR SER THR VAL PHE ASN THR THR ALA SEQRES 29 A 617 LEU GLY CYS LEU ASP ARG MET ASP LEU ARG GLY LEU ASN SEQRES 30 A 617 LEU HIS PRO THR GLN ALA ASP ALA ILE ARG CYS LEU HIS SEQRES 31 A 617 TYR ASP ASN SER THR LYS VAL ALA LEU LYS PHE SER TYR SEQRES 32 A 617 PRO TRP TRP ILE LYS ASP CYS GLY ILE THR CYS GLY GLY SEQRES 33 A 617 ALA ALA SER THR ASP LEU PRO LEU ARG THR CYS VAL TYR SEQRES 34 A 617 PRO SER TYR ASN LEU GLY ASP THR GLY GLU ALA VAL LEU SEQRES 35 A 617 LEU ALA SER TYR THR TRP SER GLN ASP ALA THR ARG ILE SEQRES 36 A 617 GLY SER LEU VAL LYS ASP ALA PRO PRO GLN PRO PRO LYS SEQRES 37 A 617 GLU ASP GLU LEU VAL GLU LEU ILE LEU GLN ASN LEU ALA SEQRES 38 A 617 ARG LEU HIS ALA GLU HIS MET THR TYR GLU LYS ILE LYS SEQRES 39 A 617 GLU ALA TYR THR GLY VAL TYR HIS ALA TYR CYS TRP ALA SEQRES 40 A 617 ASN ASP PRO ASN VAL GLY GLY ALA PHE ALA LEU PHE GLY SEQRES 41 A 617 PRO GLY GLN PHE SER ASN LEU TYR PRO TYR LEU MET ARG SEQRES 42 A 617 PRO ALA ALA GLY GLY LYS PHE HIS ILE VAL GLY GLU ALA SEQRES 43 A 617 SER SER VAL HIS HIS ALA TRP ILE ILE GLY SER LEU GLU SEQRES 44 A 617 SER ALA TYR THR ALA VAL TYR GLN PHE LEU TYR LYS TYR SEQRES 45 A 617 LYS MET TRP ASP TYR LEU ARG LEU LEU LEU GLU ARG TRP SEQRES 46 A 617 GLN TYR GLY LEU GLN GLU LEU GLU THR GLY LYS HIS GLY SEQRES 47 A 617 THR ALA HIS LEU GLN PHE ILE LEU GLY SER LEU PRO LYS SEQRES 48 A 617 GLU TYR GLN VAL LYS ILE HET FAD A 701 53 HET LYS A 702 10 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM LYS LYSINE FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 3 LYS C6 H15 N2 O2 1+ FORMUL 4 HOH *429(H2 O) HELIX 1 AA1 ASP A 5 GLU A 32 1 28 HELIX 2 AA2 LEU A 63 ILE A 67 5 5 HELIX 3 AA3 GLY A 93 LYS A 107 1 15 HELIX 4 AA4 ILE A 149 SER A 151 5 3 HELIX 5 AA5 MET A 152 THR A 162 1 11 HELIX 6 AA6 SER A 196 GLY A 200 5 5 HELIX 7 AA7 SER A 210 ASP A 229 1 20 HELIX 8 AA8 ASP A 229 LEU A 239 1 11 HELIX 9 AA9 THR A 244 GLY A 252 1 9 HELIX 10 AB1 ASP A 262 GLN A 272 1 11 HELIX 11 AB2 ALA A 282 SER A 290 1 9 HELIX 12 AB3 THR A 308 LEU A 319 1 12 HELIX 13 AB4 ALA A 364 ARG A 370 1 7 HELIX 14 AB5 LEU A 373 ASN A 377 5 5 HELIX 15 AB6 HIS A 379 LEU A 389 1 11 HELIX 16 AB7 PRO A 404 ASP A 409 1 6 HELIX 17 AB8 SER A 449 SER A 457 1 9 HELIX 18 AB9 ASP A 470 HIS A 484 1 15 HELIX 19 AC1 THR A 489 ALA A 496 1 8 HELIX 20 AC2 ALA A 507 ASP A 509 5 3 HELIX 21 AC3 GLY A 522 ARG A 533 1 12 HELIX 22 AC4 GLY A 544 SER A 548 5 5 HELIX 23 AC5 TRP A 553 TYR A 572 1 20 HELIX 24 AC6 MET A 574 GLN A 586 1 13 HELIX 25 AC7 THR A 599 LEU A 609 1 11 SHEET 1 AA1 4 LEU A 111 PHE A 116 0 SHEET 2 AA1 4 ARG A 85 VAL A 90 1 N ILE A 89 O ASP A 114 SHEET 3 AA1 4 THR A 358 ASN A 361 1 O PHE A 360 N VAL A 90 SHEET 4 AA1 4 PHE A 540 ILE A 542 1 O HIS A 541 N ASN A 361 SHEET 1 AA2 2 THR A 128 HIS A 130 0 SHEET 2 AA2 2 TYR A 138 ASP A 140 -1 O TYR A 139 N HIS A 129 SHEET 1 AA3 3 TYR A 146 PRO A 147 0 SHEET 2 AA3 3 TRP A 301 ILE A 304 -1 O TYR A 302 N TYR A 146 SHEET 3 AA3 3 LEU A 166 TYR A 169 -1 N TYR A 169 O TRP A 301 SHEET 1 AA4 4 HIS A 183 PHE A 184 0 SHEET 2 AA4 4 GLN A 178 TYR A 180 -1 N TYR A 180 O HIS A 183 SHEET 3 AA4 4 ALA A 417 THR A 420 1 O SER A 419 N LEU A 179 SHEET 4 AA4 4 THR A 426 VAL A 428 -1 O CYS A 427 N ALA A 418 SHEET 1 AA5 3 VAL A 329 ILE A 334 0 SHEET 2 AA5 3 MET A 344 ILE A 348 -1 O LYS A 347 N GLU A 330 SHEET 3 AA5 3 LYS A 351 TYR A 356 -1 O TYR A 353 N VAL A 346 SHEET 1 AA6 2 TYR A 391 ASP A 392 0 SHEET 2 AA6 2 PHE A 516 ALA A 517 -1 O PHE A 516 N ASP A 392 SHEET 1 AA7 3 ALA A 440 TRP A 448 0 SHEET 2 AA7 3 SER A 394 PHE A 401 -1 N PHE A 401 O ALA A 440 SHEET 3 AA7 3 TYR A 497 CYS A 505 -1 O HIS A 502 N ALA A 398 CISPEP 1 ASN A 295 PRO A 296 0 -8.98 CISPEP 2 PRO A 466 PRO A 467 0 -5.30 SITE 1 AC1 44 VAL A 90 GLY A 91 GLY A 93 VAL A 94 SITE 2 AC1 44 SER A 95 GLU A 117 SER A 118 GLY A 124 SITE 3 AC1 44 ARG A 125 LEU A 126 ILE A 141 GLY A 142 SITE 4 AC1 44 ALA A 143 MET A 144 ARG A 145 TYR A 146 SITE 5 AC1 44 LYS A 327 ARG A 328 VAL A 329 THR A 362 SITE 6 AC1 44 THR A 363 CYS A 367 MET A 371 SER A 394 SITE 7 AC1 44 TYR A 446 TRP A 506 ASN A 511 ALA A 515 SITE 8 AC1 44 GLY A 544 GLU A 545 ALA A 552 TRP A 553 SITE 9 AC1 44 ILE A 554 SER A 557 LYS A 702 HOH A 862 SITE 10 AC1 44 HOH A 891 HOH A 960 HOH A 966 HOH A 988 SITE 11 AC1 44 HOH A1039 HOH A1042 HOH A1046 HOH A1056 SITE 1 AC2 10 ARG A 145 THR A 276 ASP A 289 PHE A 293 SITE 2 AC2 10 TYR A 446 TRP A 448 PHE A 516 ALA A 552 SITE 3 AC2 10 TRP A 553 FAD A 701 CRYST1 94.889 130.050 94.250 90.00 90.00 90.00 C 2 2 21 8 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 0.010539 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007689 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010610 0.00000