HEADER OXIDOREDUCTASE 11-DEC-14 4X9N TITLE DITHIONITE REDUCED L-ALPHA-GLYCEROPHOSPHATE OXIDASE FROM MYCOPLASMA TITLE 2 PNEUMONIAE WITH FAD BOUND COMPND MOL_ID: 1; COMPND 2 MOLECULE: L-ALPHA-GLYCEROPHOSPHATE OXIDASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MYCOPLASMA PNEUMONIAE (STRAIN ATCC 29342 / SOURCE 3 M129); SOURCE 4 ORGANISM_TAXID: 272634; SOURCE 5 STRAIN: ATCC 29342 / M129; SOURCE 6 GENE: MPN_051, D09_ORF384, MP103; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: B834; SOURCE 10 EXPRESSION_SYSTEM_VARIANT: DE3; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS FLAVOENZYME, OXIDASE, GLYCEROL-3-PHOSPHATE OXIDASE, GLYCEROL-3- KEYWDS 2 PHOSPHATE DEHYDROGENASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR C.K.ELKHAL,K.M.KEAN,D.PARSONAGE,A.CLAIBORNE,P.A.KARPLUS REVDAT 4 27-SEP-23 4X9N 1 REMARK LINK REVDAT 3 02-SEP-15 4X9N 1 JRNL REVDAT 2 01-APR-15 4X9N 1 JRNL REVDAT 1 04-MAR-15 4X9N 0 JRNL AUTH C.K.ELKHAL,K.M.KEAN,D.PARSONAGE,S.MAENPUEN,P.CHAIYEN, JRNL AUTH 2 A.CLAIBORNE,P.A.KARPLUS JRNL TITL STRUCTURE AND PROPOSED MECHANISM OF L-ALPHA-GLYCEROPHOSPHATE JRNL TITL 2 OXIDASE FROM MYCOPLASMA PNEUMONIAE. JRNL REF FEBS J. V. 282 3030 2015 JRNL REFN ISSN 1742-464X JRNL PMID 25688572 JRNL DOI 10.1111/FEBS.13233 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 55.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 15520 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) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.146 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 831 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1118 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2380 REMARK 3 BIN FREE R VALUE SET COUNT : 54 REMARK 3 BIN FREE R VALUE : 0.3490 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3000 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 54 REMARK 3 SOLVENT ATOMS : 201 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 43.99 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 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): 0.448 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.247 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.181 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 15.508 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.969 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.943 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3183 ; 0.013 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3089 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4341 ; 1.622 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7107 ; 0.965 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 395 ; 6.683 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 133 ;39.775 ;24.887 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 549 ;15.444 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;20.860 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 495 ; 0.101 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3563 ; 0.008 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 705 ; 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): 1559 ; 2.600 ; 4.202 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1558 ; 2.599 ; 4.202 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1952 ; 3.739 ; 6.304 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1953 ; 3.738 ; 6.304 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1623 ; 3.339 ; 4.535 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1623 ; 3.339 ; 4.535 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2387 ; 5.051 ; 6.656 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3744 ; 6.550 ;34.477 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3667 ; 6.489 ;34.225 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 : 1 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 1 A 600 REMARK 3 ORIGIN FOR THE GROUP (A): 12.3671 -26.0740 43.7974 REMARK 3 T TENSOR REMARK 3 T11: 0.0358 T22: 0.0310 REMARK 3 T33: 0.0244 T12: 0.0197 REMARK 3 T13: 0.0031 T23: 0.0230 REMARK 3 L TENSOR REMARK 3 L11: 0.4691 L22: 0.1955 REMARK 3 L33: 0.7737 L12: -0.2824 REMARK 3 L13: -0.2264 L23: 0.0133 REMARK 3 S TENSOR REMARK 3 S11: 0.0296 S12: 0.0298 S13: 0.0200 REMARK 3 S21: -0.0275 S22: -0.0379 S23: -0.0231 REMARK 3 S31: 0.0143 S32: 0.0399 S33: 0.0083 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 4X9N COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-DEC-14. REMARK 100 THE DEPOSITION ID IS D_1000204853. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-SEP-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.3 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9765 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 : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 16368 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.499 REMARK 200 RESOLUTION RANGE LOW (A) : 55.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 51.10 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 28.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: PDB ENTRY 4X9M REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 53.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.66 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.68 M NACL, 2% V/V ISOPROPANOL, AND REMARK 280 0.1 M HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 3 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 Z,X,Y REMARK 290 6555 Z,-X,-Y REMARK 290 7555 -Z,-X,Y REMARK 290 8555 -Z,X,-Y REMARK 290 9555 Y,Z,X REMARK 290 10555 -Y,Z,-X REMARK 290 11555 Y,-Z,-X REMARK 290 12555 -Y,-Z,X 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 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 6 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY2 6 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 7 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY2 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY1 9 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 9 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 9 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 10 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 10 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY3 10 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY1 12 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 12 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY3 12 1.000000 0.000000 0.000000 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16470 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 NI NI A 402 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 507 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 538 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 545 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 -33 REMARK 465 GLY A -32 REMARK 465 SER A -31 REMARK 465 SER A -30 REMARK 465 HIS A -29 REMARK 465 HIS A -28 REMARK 465 HIS A -27 REMARK 465 HIS A -26 REMARK 465 HIS A -25 REMARK 465 HIS A -24 REMARK 465 SER A -23 REMARK 465 SER A -22 REMARK 465 GLY A -21 REMARK 465 LEU A -20 REMARK 465 VAL A -19 REMARK 465 PRO A -18 REMARK 465 ARG A -17 REMARK 465 GLY A -16 REMARK 465 SER A -15 REMARK 465 HIS A -14 REMARK 465 MET A -13 REMARK 465 ALA A -12 REMARK 465 SER A -11 REMARK 465 MET A -10 REMARK 465 THR A -9 REMARK 465 GLY A -8 REMARK 465 GLY A -7 REMARK 465 GLN A -6 REMARK 465 GLN A -5 REMARK 465 MET A -4 REMARK 465 GLY A -3 REMARK 465 ARG A -2 REMARK 465 GLY A -1 REMARK 465 SER A 0 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS A 79 CG CD CE NZ REMARK 470 LYS A 298 CG CD CE NZ 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 OD1 ASN A 116 O HOH A 608 2.18 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 GLU A 41 -117.72 -112.75 REMARK 500 THR A 76 -61.80 -124.82 REMARK 500 ASN A 174 46.06 30.76 REMARK 500 LEU A 243 122.69 -36.30 REMARK 500 ASP A 337 106.10 -177.06 REMARK 500 PRO A 349 61.29 -110.38 REMARK 500 ASN A 366 61.19 65.80 REMARK 500 TRP A 375 -82.60 -74.55 REMARK 500 ASN A 376 -32.51 83.96 REMARK 500 REMARK 500 REMARK: NULL 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 NI A 402 NI REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 59 NE2 REMARK 620 2 HIS A 59 NE2 0.0 REMARK 620 3 HOH A 538 O 118.6 118.6 REMARK 620 4 HOH A 538 O 118.6 118.6 0.0 REMARK 620 N 1 2 3 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 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NI A 402 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4X9M RELATED DB: PDB DBREF 4X9N A 1 384 UNP P75063 Y051_MYCPN 1 384 SEQADV 4X9N MET A -33 UNP P75063 INITIATING METHIONINE SEQADV 4X9N GLY A -32 UNP P75063 EXPRESSION TAG SEQADV 4X9N SER A -31 UNP P75063 EXPRESSION TAG SEQADV 4X9N SER A -30 UNP P75063 EXPRESSION TAG SEQADV 4X9N HIS A -29 UNP P75063 EXPRESSION TAG SEQADV 4X9N HIS A -28 UNP P75063 EXPRESSION TAG SEQADV 4X9N HIS A -27 UNP P75063 EXPRESSION TAG SEQADV 4X9N HIS A -26 UNP P75063 EXPRESSION TAG SEQADV 4X9N HIS A -25 UNP P75063 EXPRESSION TAG SEQADV 4X9N HIS A -24 UNP P75063 EXPRESSION TAG SEQADV 4X9N SER A -23 UNP P75063 EXPRESSION TAG SEQADV 4X9N SER A -22 UNP P75063 EXPRESSION TAG SEQADV 4X9N GLY A -21 UNP P75063 EXPRESSION TAG SEQADV 4X9N LEU A -20 UNP P75063 EXPRESSION TAG SEQADV 4X9N VAL A -19 UNP P75063 EXPRESSION TAG SEQADV 4X9N PRO A -18 UNP P75063 EXPRESSION TAG SEQADV 4X9N ARG A -17 UNP P75063 EXPRESSION TAG SEQADV 4X9N GLY A -16 UNP P75063 EXPRESSION TAG SEQADV 4X9N SER A -15 UNP P75063 EXPRESSION TAG SEQADV 4X9N HIS A -14 UNP P75063 EXPRESSION TAG SEQADV 4X9N MET A -13 UNP P75063 EXPRESSION TAG SEQADV 4X9N ALA A -12 UNP P75063 EXPRESSION TAG SEQADV 4X9N SER A -11 UNP P75063 EXPRESSION TAG SEQADV 4X9N MET A -10 UNP P75063 EXPRESSION TAG SEQADV 4X9N THR A -9 UNP P75063 EXPRESSION TAG SEQADV 4X9N GLY A -8 UNP P75063 EXPRESSION TAG SEQADV 4X9N GLY A -7 UNP P75063 EXPRESSION TAG SEQADV 4X9N GLN A -6 UNP P75063 EXPRESSION TAG SEQADV 4X9N GLN A -5 UNP P75063 EXPRESSION TAG SEQADV 4X9N MET A -4 UNP P75063 EXPRESSION TAG SEQADV 4X9N GLY A -3 UNP P75063 EXPRESSION TAG SEQADV 4X9N ARG A -2 UNP P75063 EXPRESSION TAG SEQADV 4X9N GLY A -1 UNP P75063 EXPRESSION TAG SEQADV 4X9N SER A 0 UNP P75063 EXPRESSION TAG SEQRES 1 A 418 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 418 LEU VAL PRO ARG GLY SER HIS MET ALA SER MET THR GLY SEQRES 3 A 418 GLY GLN GLN MET GLY ARG GLY SER MET GLU THR ARG ASP SEQRES 4 A 418 VAL LEU ILE VAL GLY GLY GLY VAL ILE GLY CYS ALA THR SEQRES 5 A 418 ALA TYR GLU LEU SER GLN TYR LYS LEU LYS VAL THR LEU SEQRES 6 A 418 VAL GLU LYS HIS HIS TYR LEU ALA GLN GLU THR SER HIS SEQRES 7 A 418 ALA ASN SER GLY VAL ILE HIS THR GLY ILE ASP PRO ASN SEQRES 8 A 418 PRO HIS LYS LEU THR ALA LYS TYR ASN ILE LEU GLY LYS SEQRES 9 A 418 LYS LEU TRP LEU ASN THR TYR PHE LYS ARG LEU GLY PHE SEQRES 10 A 418 PRO ARG GLN LYS ILE ARG THR LEU ILE VAL ALA PHE ASN SEQRES 11 A 418 GLU MET GLU ARG GLU GLN LEU GLU VAL LEU LYS GLN ARG SEQRES 12 A 418 GLY ILE ALA ASN GLN ILE ASN LEU GLU ASP ILE GLN MET SEQRES 13 A 418 LEU SER LYS GLU GLU THR LEU LYS LEU GLU PRO TYR VAL SEQRES 14 A 418 ASN PRO GLU ILE VAL ALA GLY LEU LYS ILE GLU GLY SER SEQRES 15 A 418 TRP ALA ILE ASP PRO VAL LEU ALA SER LYS CYS LEU ALA SEQRES 16 A 418 LEU ALA ALA GLN GLN ASN LYS VAL GLN ILE CYS THR ASN SEQRES 17 A 418 THR GLU VAL THR ASN ILE SER LYS GLN VAL ASP GLY THR SEQRES 18 A 418 TYR LEU VAL TRP THR ASN ASN GLU THR THR PRO SER PHE SEQRES 19 A 418 LYS VAL LYS LYS ILE ILE ASP ALA ALA GLY HIS TYR ALA SEQRES 20 A 418 ASP TYR LEU ALA HIS LEU ALA LYS ALA ASP ASP PHE GLU SEQRES 21 A 418 GLN THR THR ARG ARG GLY GLN TYR VAL VAL VAL THR ASN SEQRES 22 A 418 GLN GLY GLU LEU HIS LEU ASN SER MET VAL PHE MET VAL SEQRES 23 A 418 PRO THR ILE HIS GLY LYS GLY VAL ILE VAL SER PRO MET SEQRES 24 A 418 LEU ASP GLY ASN PHE LEU VAL GLY PRO THR ALA LEU ASP SEQRES 25 A 418 GLY VAL ASP LYS GLU ALA THR ARG TYR ILE THR LYS ASP SEQRES 26 A 418 ALA PRO CYS MET LEU THR LYS ILE GLY LYS HIS MET VAL SEQRES 27 A 418 PRO SER LEU ASN ILE ASN ASN ALA LEU ILE SER PHE ALA SEQRES 28 A 418 GLY SER ARG PRO ILE ASP LYS ALA THR ASN ASP PHE ILE SEQRES 29 A 418 ILE ARG VAL ALA HIS ASN ASP PRO ASP PHE VAL ILE LEU SEQRES 30 A 418 GLY GLY MET LYS SER PRO GLY LEU THR ALA ALA PRO ALA SEQRES 31 A 418 ILE VAL ARG GLU ALA VAL ARG LEU LEU ASN TRP LYS LEU SEQRES 32 A 418 THR LYS LYS PRO ASN TRP ASN GLY LYS TYR ASN LEU PRO SEQRES 33 A 418 TRP ILE HET FAD A 401 53 HET NI A 402 1 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM NI NICKEL (II) ION FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 3 NI NI 2+ FORMUL 4 HOH *201(H2 O) HELIX 1 AA1 GLY A 12 SER A 23 1 12 HELIX 2 AA2 GLU A 41 ALA A 45 5 5 HELIX 3 AA3 LYS A 60 THR A 76 1 17 HELIX 4 AA4 THR A 76 ARG A 80 1 5 HELIX 5 AA5 ASN A 96 ASN A 113 1 18 HELIX 6 AA6 ASN A 116 GLU A 118 5 3 HELIX 7 AA7 LYS A 125 GLU A 132 1 8 HELIX 8 AA8 ASP A 152 ASN A 167 1 16 HELIX 9 AA9 ALA A 209 HIS A 211 5 3 HELIX 10 AB1 TYR A 212 ALA A 220 1 9 HELIX 11 AB2 VAL A 252 GLY A 257 1 6 HELIX 12 AB3 ASP A 281 THR A 285 5 5 HELIX 13 AB4 ASP A 291 VAL A 304 1 14 HELIX 14 AB5 PRO A 349 LEU A 364 1 16 SHEET 1 AA1 6 GLN A 170 CYS A 172 0 SHEET 2 AA1 6 VAL A 29 VAL A 32 1 N LEU A 31 O GLN A 170 SHEET 3 AA1 6 GLU A 2 VAL A 9 1 N ILE A 8 O THR A 30 SHEET 4 AA1 6 PHE A 200 ASP A 207 1 O ILE A 206 N LEU A 7 SHEET 5 AA1 6 TYR A 188 THR A 192 -1 N TYR A 188 O VAL A 202 SHEET 6 AA1 6 VAL A 177 LYS A 182 -1 N ASN A 179 O TRP A 191 SHEET 1 AA2 6 GLN A 170 CYS A 172 0 SHEET 2 AA2 6 VAL A 29 VAL A 32 1 N LEU A 31 O GLN A 170 SHEET 3 AA2 6 GLU A 2 VAL A 9 1 N ILE A 8 O THR A 30 SHEET 4 AA2 6 PHE A 200 ASP A 207 1 O ILE A 206 N LEU A 7 SHEET 5 AA2 6 ASP A 337 GLY A 344 1 O VAL A 341 N ASP A 207 SHEET 6 AA2 6 ILE A 330 ALA A 334 -1 N ARG A 332 O ILE A 342 SHEET 1 AA3 3 VAL A 49 ILE A 50 0 SHEET 2 AA3 3 TRP A 149 ILE A 151 -1 O TRP A 149 N ILE A 50 SHEET 3 AA3 3 ARG A 85 LYS A 87 -1 N GLN A 86 O ALA A 150 SHEET 1 AA4 2 LEU A 81 GLY A 82 0 SHEET 2 AA4 2 TYR A 379 ASN A 380 1 O TYR A 379 N GLY A 82 SHEET 1 AA5 8 ILE A 120 SER A 124 0 SHEET 2 AA5 8 ALA A 141 ILE A 145 -1 O GLY A 142 N LEU A 123 SHEET 3 AA5 8 THR A 90 ALA A 94 -1 N THR A 90 O ILE A 145 SHEET 4 AA5 8 MET A 248 MET A 251 1 O MET A 248 N LEU A 91 SHEET 5 AA5 8 ILE A 261 PRO A 264 -1 O VAL A 262 N VAL A 249 SHEET 6 AA5 8 PHE A 270 GLY A 273 -1 O GLY A 273 N ILE A 261 SHEET 7 AA5 8 GLN A 227 VAL A 237 -1 N VAL A 237 O PHE A 270 SHEET 8 AA5 8 LEU A 277 ASP A 278 -1 O LEU A 277 N ARG A 231 SHEET 1 AA6 8 ILE A 120 SER A 124 0 SHEET 2 AA6 8 ALA A 141 ILE A 145 -1 O GLY A 142 N LEU A 123 SHEET 3 AA6 8 THR A 90 ALA A 94 -1 N THR A 90 O ILE A 145 SHEET 4 AA6 8 MET A 248 MET A 251 1 O MET A 248 N LEU A 91 SHEET 5 AA6 8 ILE A 261 PRO A 264 -1 O VAL A 262 N VAL A 249 SHEET 6 AA6 8 PHE A 270 GLY A 273 -1 O GLY A 273 N ILE A 261 SHEET 7 AA6 8 GLN A 227 VAL A 237 -1 N VAL A 237 O PHE A 270 SHEET 8 AA6 8 ALA A 312 ASP A 323 -1 O GLY A 318 N GLY A 232 SSBOND 1 CYS A 294 CYS A 294 1555 2555 2.08 LINK NE2 HIS A 59 NI NI A 402 1555 1555 2.13 LINK NE2 HIS A 59 NI NI A 402 1555 6555 2.13 LINK NI NI A 402 O HOH A 538 1555 1555 1.91 LINK NI NI A 402 O HOH A 538 1555 6555 1.91 CISPEP 1 GLY A 273 PRO A 274 0 6.34 CISPEP 2 SER A 348 PRO A 349 0 7.25 SITE 1 AC1 38 GLY A 10 GLY A 12 VAL A 13 ILE A 14 SITE 2 AC1 38 GLU A 33 LYS A 34 HIS A 35 GLU A 41 SITE 3 AC1 38 THR A 42 SER A 43 ALA A 45 ASN A 46 SITE 4 AC1 38 SER A 47 VAL A 49 HIS A 51 THR A 175 SITE 5 AC1 38 GLU A 176 VAL A 177 ALA A 208 ALA A 209 SITE 6 AC1 38 GLY A 210 TYR A 212 TYR A 234 GLY A 318 SITE 7 AC1 38 SER A 319 ARG A 320 MET A 346 LYS A 347 SITE 8 AC1 38 SER A 348 PRO A 349 GLY A 350 LEU A 351 SITE 9 AC1 38 THR A 352 HOH A 549 HOH A 556 HOH A 558 SITE 10 AC1 38 HOH A 563 HOH A 569 SITE 1 AC2 2 HIS A 59 HOH A 538 CRYST1 111.605 111.605 111.605 90.00 90.00 90.00 P 2 3 12 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 0.008960 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008960 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008960 0.00000