HEADER OXIDOREDUCTASE 18-FEB-15 4YBN TITLE STRUCTURE OF THE FAD AND HEME BINDING PROTEIN MSMEG_4975 FROM TITLE 2 MYCOBACTERIUM SMEGMATIS COMPND MOL_ID: 1; COMPND 2 MOLECULE: FLAVIN-NUCLEOTIDE-BINDING PROTEIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: PYRIDOXAMINE 5'-PHOSPHATE OXIDASE-RELATED,FMN-BINDING COMPND 5 PROTEIN; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOBACTERIUM SMEGMATIS (STRAIN ATCC 700084 / SOURCE 3 MC(2)155); SOURCE 4 ORGANISM_TAXID: 246196; SOURCE 5 STRAIN: ATCC 700084 / MC(2)155; SOURCE 6 GENE: MSMEG_4975, MSMEI_4848, LJ00_24605; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS OXIDOREDUCTASE, FAD, HEME, SPLIT BETA-BARREL EXPDTA X-RAY DIFFRACTION AUTHOR F.H.AHMED,P.D.CARR,C.J.JACKSON REVDAT 4 27-SEP-23 4YBN 1 LINK REVDAT 3 01-JAN-20 4YBN 1 REMARK REVDAT 2 04-NOV-15 4YBN 1 JRNL SHEET REVDAT 1 21-OCT-15 4YBN 0 JRNL AUTH F.H.AHMED,P.D.CARR,B.M.LEE,L.AFRIAT-JURNOU,A.E.MOHAMED, JRNL AUTH 2 N.S.HONG,J.FLANAGAN,M.C.TAYLOR,C.GREENING,C.J.JACKSON JRNL TITL SEQUENCE-STRUCTURE-FUNCTION CLASSIFICATION OF A JRNL TITL 2 CATALYTICALLY DIVERSE OXIDOREDUCTASE SUPERFAMILY IN JRNL TITL 3 MYCOBACTERIA. JRNL REF J.MOL.BIOL. V. 427 3554 2015 JRNL REFN ESSN 1089-8638 JRNL PMID 26434506 JRNL DOI 10.1016/J.JMB.2015.09.021 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 44.73 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 33553 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.176 REMARK 3 R VALUE (WORKING SET) : 0.174 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1749 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 1.9490 - 1.9000 0.99 2455 125 0.2740 0.3130 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 SOLVENT RADIUS : 1.20 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.117 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 33.33 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.88000 REMARK 3 B22 (A**2) : 2.21000 REMARK 3 B33 (A**2) : -0.30000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.15000 REMARK 3 B23 (A**2) : 0.00000 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 4YBN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-FEB-15. REMARK 100 THE DEPOSITION ID IS D_1000207085. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 14-FEB-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 3.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : AUSTRALIAN SYNCHROTRON REMARK 200 BEAMLINE : MX2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9655 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 35306 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 44.730 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 7.500 REMARK 200 R MERGE (I) : 0.10100 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.0000 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) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.2 REMARK 200 DATA REDUNDANCY IN SHELL : 7.60 REMARK 200 R MERGE FOR SHELL (I) : 1.10900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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: PDB ID: 2FUR REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.47 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.48 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG1500, 4% MPD, 0.1 M CITRIC REMARK 280 ACID, PH 3.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 42.36100 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 29.93800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 42.36100 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 29.93800 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 12410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 17060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -153.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 2 REMARK 465 THR A 3 REMARK 465 ASP A 4 REMARK 465 VAL A 5 REMARK 465 SER A 6 REMARK 465 LYS A 7 REMARK 465 PRO A 8 REMARK 465 ARG A 223 REMARK 465 ALA A 224 REMARK 465 ARG A 225 REMARK 465 MET B 2 REMARK 465 THR B 3 REMARK 465 ASP B 4 REMARK 465 VAL B 5 REMARK 465 SER B 6 REMARK 465 LYS B 7 REMARK 465 PRO B 8 REMARK 465 SER B 9 REMARK 465 THR B 10 REMARK 465 ARG B 11 REMARK 465 VAL B 12 REMARK 465 THR B 13 REMARK 465 ARG B 14 REMARK 465 LEU B 15 REMARK 465 ASP B 16 REMARK 465 THR B 222 REMARK 465 ARG B 223 REMARK 465 ALA B 224 REMARK 465 ARG B 225 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 481 O HOH B 483 2.15 REMARK 500 OH TYR B 123 O HOH B 401 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 ALA B 204 O ALA B 204 2656 1.94 REMARK 500 O HOH A 496 O HOH B 444 3445 2.08 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 TRP A 70 CB TRP A 70 CG -0.147 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 B 130 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG B 130 NE - CZ - NH2 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 SER A 100 -166.64 -177.54 REMARK 500 ASP A 172 69.75 -108.33 REMARK 500 ASP B 43 61.95 34.36 REMARK 500 SER B 100 -169.46 -168.13 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 B 555 DISTANCE = 6.00 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM A 304 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 63 NE2 REMARK 620 2 HEM A 304 NA 109.0 REMARK 620 3 HEM A 304 NB 76.8 89.8 REMARK 620 4 HEM A 304 NC 73.5 175.9 87.7 REMARK 620 5 HEM A 304 ND 105.8 91.1 176.7 91.2 REMARK 620 6 HOH A 490 O 178.6 72.2 102.7 105.2 74.6 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NI A 301 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 125 OD2 REMARK 620 2 SO4 A 302 O2 90.7 REMARK 620 3 HOH B 449 O 118.3 124.3 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 HEM B 301 FE REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 422 O REMARK 620 2 HEM B 301 NA 79.1 REMARK 620 3 HEM B 301 NB 88.0 89.5 REMARK 620 4 HEM B 301 NC 95.9 175.0 89.6 REMARK 620 5 HEM B 301 ND 87.7 90.7 175.6 89.8 REMARK 620 6 HIS B 63 NE2 172.3 106.8 87.0 78.1 97.1 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ACT A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue HEM B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FAD B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FAD B 305 DBREF 4YBN A 2 225 UNP A0R238 A0R238_MYCS2 1 224 DBREF 4YBN B 2 225 UNP A0R238 A0R238_MYCS2 1 224 SEQRES 1 A 224 MET THR ASP VAL SER LYS PRO SER THR ARG VAL THR ARG SEQRES 2 A 224 LEU ASP GLU LYS GLN SER THR SER ARG GLU ARG LEU ASP SEQRES 3 A 224 ASP LEU LEU ASP THR ILE PRO LEU ALA THR VAL ALA LEU SEQRES 4 A 224 VAL ARG ASP GLY HIS PRO VAL ALA PHE PRO ILE GLY PHE SEQRES 5 A 224 GLY ARG VAL GLY ASP GLU LEU VAL ILE HIS GLY SER THR SEQRES 6 A 224 GLY SER PRO TRP LEU ARG ALA LEU ALA GLU GLY ALA PRO SEQRES 7 A 224 ALA ALA VAL SER VAL THR ALA LEU ASP GLY VAL VAL VAL SEQRES 8 A 224 ALA ARG SER SER PHE GLU SER SER PHE ARG TYR ARG SER SEQRES 9 A 224 ALA THR LEU PHE GLY THR PHE GLU VAL ILE ALA ASP ASP SEQRES 10 A 224 ALA LYS ARG GLY TYR LEU ASP ALA LEU THR ASP ARG PHE SEQRES 11 A 224 ILE PRO GLY ARG THR ALA GLU LEU ARG ALA SER THR ARG SEQRES 12 A 224 LYS GLU LEU ALA ALA THR LEU ALA LEU ALA LEU ALA ILE SEQRES 13 A 224 GLY ASP ASP ASN TRP SER LEU LYS LEU SER GLU GLY TRP SEQRES 14 A 224 PRO ASP ASP ALA ASP GLU ASP ILE ALA ALA GLY GLY TRP SEQRES 15 A 224 ALA GLY VAL VAL PRO LEU THR THR GLN TYR GLY ALA PRO SEQRES 16 A 224 LEU THR ALA PRO ASP VAL ALA ALA GLY THR PRO LEU PRO SEQRES 17 A 224 PRO SER VAL ARG GLY MET THR GLY GLU LEU ARG ASN THR SEQRES 18 A 224 ARG ALA ARG SEQRES 1 B 224 MET THR ASP VAL SER LYS PRO SER THR ARG VAL THR ARG SEQRES 2 B 224 LEU ASP GLU LYS GLN SER THR SER ARG GLU ARG LEU ASP SEQRES 3 B 224 ASP LEU LEU ASP THR ILE PRO LEU ALA THR VAL ALA LEU SEQRES 4 B 224 VAL ARG ASP GLY HIS PRO VAL ALA PHE PRO ILE GLY PHE SEQRES 5 B 224 GLY ARG VAL GLY ASP GLU LEU VAL ILE HIS GLY SER THR SEQRES 6 B 224 GLY SER PRO TRP LEU ARG ALA LEU ALA GLU GLY ALA PRO SEQRES 7 B 224 ALA ALA VAL SER VAL THR ALA LEU ASP GLY VAL VAL VAL SEQRES 8 B 224 ALA ARG SER SER PHE GLU SER SER PHE ARG TYR ARG SER SEQRES 9 B 224 ALA THR LEU PHE GLY THR PHE GLU VAL ILE ALA ASP ASP SEQRES 10 B 224 ALA LYS ARG GLY TYR LEU ASP ALA LEU THR ASP ARG PHE SEQRES 11 B 224 ILE PRO GLY ARG THR ALA GLU LEU ARG ALA SER THR ARG SEQRES 12 B 224 LYS GLU LEU ALA ALA THR LEU ALA LEU ALA LEU ALA ILE SEQRES 13 B 224 GLY ASP ASP ASN TRP SER LEU LYS LEU SER GLU GLY TRP SEQRES 14 B 224 PRO ASP ASP ALA ASP GLU ASP ILE ALA ALA GLY GLY TRP SEQRES 15 B 224 ALA GLY VAL VAL PRO LEU THR THR GLN TYR GLY ALA PRO SEQRES 16 B 224 LEU THR ALA PRO ASP VAL ALA ALA GLY THR PRO LEU PRO SEQRES 17 B 224 PRO SER VAL ARG GLY MET THR GLY GLU LEU ARG ASN THR SEQRES 18 B 224 ARG ALA ARG HET NI A 301 1 HET SO4 A 302 5 HET ACT A 303 4 HET HEM A 304 43 HET HEM B 301 43 HET FAD B 302 53 HET NI B 303 1 HET SO4 B 304 5 HET FAD B 305 53 HETNAM NI NICKEL (II) ION HETNAM SO4 SULFATE ION HETNAM ACT ACETATE ION HETNAM HEM PROTOPORPHYRIN IX CONTAINING FE HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETSYN HEM HEME FORMUL 3 NI 2(NI 2+) FORMUL 4 SO4 2(O4 S 2-) FORMUL 5 ACT C2 H3 O2 1- FORMUL 6 HEM 2(C34 H32 FE N4 O4) FORMUL 8 FAD 2(C27 H33 N9 O15 P2) FORMUL 12 HOH *324(H2 O) HELIX 1 AA1 LEU A 15 GLN A 19 5 5 HELIX 2 AA2 SER A 22 ASP A 31 1 10 HELIX 3 AA3 SER A 68 GLU A 76 1 9 HELIX 4 AA4 ALA A 116 ILE A 132 1 17 HELIX 5 AA5 GLY A 134 LEU A 139 1 6 HELIX 6 AA6 THR A 143 ALA A 149 1 7 HELIX 7 AA7 ALA A 174 ALA A 180 1 7 HELIX 8 AA8 PRO A 209 GLY A 214 1 6 HELIX 9 AA9 SER B 22 ASP B 31 1 10 HELIX 10 AB1 SER B 68 GLU B 76 1 9 HELIX 11 AB2 ALA B 116 ILE B 132 1 17 HELIX 12 AB3 THR B 143 ALA B 149 1 7 HELIX 13 AB4 ALA B 174 GLY B 181 1 8 HELIX 14 AB5 PRO B 209 GLY B 214 1 6 SHEET 1 AA1 5 TRP A 162 SER A 167 0 SHEET 2 AA1 5 SER A 100 GLY A 110 -1 N TYR A 103 O SER A 167 SHEET 3 AA1 5 ALA A 80 VAL A 92 -1 N VAL A 91 O SER A 100 SHEET 4 AA1 5 LEU A 35 ARG A 42 -1 N THR A 37 O SER A 83 SHEET 5 AA1 5 HIS A 45 GLY A 52 -1 O PHE A 49 N VAL A 38 SHEET 1 AA2 5 HIS A 45 GLY A 52 0 SHEET 2 AA2 5 LEU A 35 ARG A 42 -1 N VAL A 38 O PHE A 49 SHEET 3 AA2 5 ALA A 80 VAL A 92 -1 O SER A 83 N THR A 37 SHEET 4 AA2 5 GLY A 185 TYR A 193 -1 O VAL A 187 N VAL A 90 SHEET 5 AA2 5 LEU B 197 THR B 198 -1 O LEU B 197 N VAL A 186 SHEET 1 AA3 6 LEU B 197 THR B 198 0 SHEET 2 AA3 6 GLY A 185 TYR A 193 -1 N VAL A 186 O LEU B 197 SHEET 3 AA3 6 GLY B 185 TYR B 193 -1 O THR B 190 N GLN A 192 SHEET 4 AA3 6 PRO B 79 VAL B 92 -1 N VAL B 92 O GLY B 185 SHEET 5 AA3 6 LEU B 35 ARG B 42 -1 N ALA B 39 O ALA B 81 SHEET 6 AA3 6 HIS B 45 GLY B 52 -1 O HIS B 45 N ARG B 42 SHEET 1 AA4 6 LEU A 197 THR A 198 0 SHEET 2 AA4 6 GLY B 185 TYR B 193 -1 O VAL B 186 N LEU A 197 SHEET 3 AA4 6 PRO B 79 VAL B 92 -1 N VAL B 92 O GLY B 185 SHEET 4 AA4 6 SER B 100 THR B 111 -1 O SER B 100 N VAL B 91 SHEET 5 AA4 6 TRP B 162 SER B 167 -1 O LYS B 165 N SER B 105 SHEET 6 AA4 6 GLN B 19 SER B 20 -1 N SER B 20 O LEU B 164 SHEET 1 AA5 4 GLY A 54 VAL A 56 0 SHEET 2 AA5 4 GLU A 59 SER A 65 -1 O GLU A 59 N VAL A 56 SHEET 3 AA5 4 THR A 150 ALA A 156 -1 O LEU A 155 N LEU A 60 SHEET 4 AA5 4 GLU A 113 VAL A 114 -1 N GLU A 113 O ALA A 154 SHEET 1 AA6 4 GLY B 54 VAL B 56 0 SHEET 2 AA6 4 GLU B 59 SER B 65 -1 O GLU B 59 N VAL B 56 SHEET 3 AA6 4 THR B 150 ALA B 156 -1 O LEU B 151 N GLY B 64 SHEET 4 AA6 4 GLU B 113 VAL B 114 -1 N GLU B 113 O ALA B 154 LINK NE2 HIS A 63 FE HEM A 304 1555 1555 2.49 LINK OD2 ASP A 125 NI NI A 301 1555 1555 1.92 LINK NI NI A 301 O2 SO4 A 302 1555 1555 2.60 LINK NI NI A 301 O HOH B 449 1555 3445 2.53 LINK FE HEM A 304 O HOH A 490 1555 1555 2.66 LINK O HOH A 422 FE HEM B 301 1555 1555 2.33 LINK NE2 HIS B 63 FE HEM B 301 1555 1555 2.19 LINK OD2 ASP B 125 NI NI B 303 1555 1555 2.18 SITE 1 AC1 5 ARG A 121 ASP A 125 SO4 A 302 GLY B 57 SITE 2 AC1 5 HOH B 449 SITE 1 AC2 6 ARG A 121 ASP A 125 NI A 301 HOH A 458 SITE 2 AC2 6 ARG B 55 GLY B 57 SITE 1 AC3 8 VAL A 56 TYR A 123 HOH A 406 HOH A 426 SITE 2 AC3 8 HOH A 496 GLY B 122 TYR B 123 HOH B 469 SITE 1 AC4 19 HIS A 63 SER A 65 LEU A 124 THR A 128 SITE 2 AC4 19 PHE A 131 SER A 142 ALA A 149 THR A 150 SITE 3 AC4 19 HOH A 490 HOH A 510 SER B 96 PHE B 97 SITE 4 AC4 19 SER B 99 SER B 100 PHE B 101 TYR B 103 SITE 5 AC4 19 LYS B 165 FAD B 302 HOH B 405 SITE 1 AC5 22 ARG A 14 LEU A 15 LYS A 18 SER A 96 SITE 2 AC5 22 PHE A 97 SER A 99 SER A 100 PHE A 101 SITE 3 AC5 22 TYR A 103 LYS A 165 HOH A 422 HOH A 539 SITE 4 AC5 22 HIS B 63 SER B 65 THR B 128 PHE B 131 SITE 5 AC5 22 SER B 142 ALA B 149 THR B 150 FAD B 305 SITE 6 AC5 22 HOH B 472 HOH B 522 SITE 1 AC6 20 LEU A 35 PRO A 50 ILE A 51 GLY A 52 SITE 2 AC6 20 HIS A 63 GLY A 64 SER A 68 PRO A 69 SITE 3 AC6 20 TRP A 70 HEM A 304 HOH A 425 GLN B 19 SITE 4 AC6 20 TYR B 103 SER B 105 THR B 107 PHE B 109 SITE 5 AC6 20 SER B 163 LYS B 165 HOH B 405 HOH B 511 SITE 1 AC7 2 ASP B 125 SO4 B 304 SITE 1 AC8 6 ARG A 55 GLY A 57 HOH A 447 ARG B 121 SITE 2 AC8 6 ASP B 125 NI B 303 SITE 1 AC9 27 SER A 9 THR A 10 ARG A 11 VAL A 12 SITE 2 AC9 27 THR A 13 ARG A 14 TYR A 103 SER A 105 SITE 3 AC9 27 THR A 107 SER A 163 LYS A 165 LEU B 35 SITE 4 AC9 27 PHE B 49 PRO B 50 ILE B 51 GLY B 52 SITE 5 AC9 27 HIS B 63 GLY B 64 SER B 68 PRO B 69 SITE 6 AC9 27 TRP B 70 HEM B 301 HOH B 425 HOH B 436 SITE 7 AC9 27 HOH B 453 HOH B 491 HOH B 495 CRYST1 84.722 59.876 89.658 90.00 93.83 90.00 C 1 2 1 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 0.011803 0.000000 0.000791 0.00000 SCALE2 0.000000 0.016701 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011179 0.00000