HEADER OXIDOREDUCTASE 11-DEC-14 4X9M TITLE OXIDIZED L-ALPHA-GLYCEROPHOSPHATE OXIDASE FROM MYCOPLASMA PNEUMONIAE TITLE 2 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 3 02-SEP-15 4X9M 1 JRNL REVDAT 2 01-APR-15 4X9M 1 JRNL REVDAT 1 04-MAR-15 4X9M 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. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.90 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 17440 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) : 0.148 REMARK 3 FREE R VALUE : 0.204 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 923 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) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.46 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1259 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.58 REMARK 3 BIN R VALUE (WORKING SET) : 0.2150 REMARK 3 BIN FREE R VALUE SET COUNT : 58 REMARK 3 BIN FREE R VALUE : 0.2460 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 : 64 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) : 37.40 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): 0.318 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.217 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.150 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 12.320 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3174 ; 0.015 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 3080 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4328 ; 1.802 ; 1.972 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7085 ; 0.986 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 393 ; 6.853 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 133 ;39.262 ;24.887 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 546 ;16.234 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 13 ;21.569 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 494 ; 0.114 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3549 ; 0.010 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 703 ; 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): 1554 ; 2.437 ; 3.486 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1553 ; 2.435 ; 3.485 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1944 ; 3.370 ; 5.227 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1945 ; 3.370 ; 5.227 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1619 ; 3.673 ; 3.875 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1619 ; 3.673 ; 3.875 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2382 ; 5.494 ; 5.641 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 3701 ; 7.172 ;29.137 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 3626 ; 7.111 ;28.792 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): 12.3420 -25.9423 43.7699 REMARK 3 T TENSOR REMARK 3 T11: 0.0426 T22: 0.0276 REMARK 3 T33: 0.0440 T12: 0.0216 REMARK 3 T13: -0.0004 T23: 0.0199 REMARK 3 L TENSOR REMARK 3 L11: 0.5300 L22: 0.4002 REMARK 3 L33: 1.0753 L12: -0.2422 REMARK 3 L13: -0.3146 L23: 0.0808 REMARK 3 S TENSOR REMARK 3 S11: 0.0355 S12: 0.0335 S13: 0.0160 REMARK 3 S21: -0.0267 S22: -0.0612 S23: -0.0379 REMARK 3 S31: 0.0132 S32: 0.0781 S33: 0.0257 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 4X9M 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_1000205271. 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 : 18401 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 23.40 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.0 REMARK 200 DATA REDUNDANCY IN SHELL : 23.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.400 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: 3DME REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.56 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2.68 M NACL, 2% V/V ISOPROPANOL, 0.1 M REMARK 280 HEPES PH 7.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 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 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 512 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 541 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 C2 G3P A 403 O HOH A 557 0.94 REMARK 500 C3 G3P A 403 O HOH A 557 1.03 REMARK 500 O2 G3P A 403 O HOH A 557 1.39 REMARK 500 CZ ARG A 320 O3P G3P A 403 1.57 REMARK 500 NE ARG A 320 O4P G3P A 403 1.64 REMARK 500 O1 G3P A 403 O HOH A 621 1.76 REMARK 500 O1P G3P A 403 O HOH A 557 1.80 REMARK 500 CB LYS A 258 O2P G3P A 403 1.89 REMARK 500 O4P G3P A 403 O HOH A 561 1.95 REMARK 500 NE ARG A 320 O3P G3P A 403 2.12 REMARK 500 CZ ARG A 320 P G3P A 403 2.14 REMARK 500 O HOH A 515 O HOH A 538 2.19 REMARK 500 NE ARG A 320 P G3P A 403 2.19 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 -117.40 -114.47 REMARK 500 ALA A 45 73.33 -107.44 REMARK 500 THR A 76 -54.62 -129.27 REMARK 500 ASN A 194 19.28 58.87 REMARK 500 THR A 228 -169.94 -112.29 REMARK 500 LEU A 243 125.70 -31.85 REMARK 500 THR A 254 -33.63 -39.01 REMARK 500 ASP A 337 101.56 -169.95 REMARK 500 PRO A 349 59.33 -109.05 REMARK 500 REMARK 500 REMARK: NULL REMARK 615 REMARK 615 ZERO OCCUPANCY ATOM REMARK 615 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 615 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 615 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 615 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 615 M RES C SSEQI REMARK 615 G3P A 403 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 HOH A 541 O 115.9 REMARK 620 3 HIS A 59 NE2 0.0 115.9 REMARK 620 4 HOH A 541 O 115.9 0.0 115.9 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: 4X9N RELATED DB: PDB DBREF 4X9M A 1 384 UNP P75063 Y051_MYCPN 1 384 SEQADV 4X9M MET A -33 UNP P75063 INITIATING METHIONINE SEQADV 4X9M GLY A -32 UNP P75063 EXPRESSION TAG SEQADV 4X9M SER A -31 UNP P75063 EXPRESSION TAG SEQADV 4X9M SER A -30 UNP P75063 EXPRESSION TAG SEQADV 4X9M HIS A -29 UNP P75063 EXPRESSION TAG SEQADV 4X9M HIS A -28 UNP P75063 EXPRESSION TAG SEQADV 4X9M HIS A -27 UNP P75063 EXPRESSION TAG SEQADV 4X9M HIS A -26 UNP P75063 EXPRESSION TAG SEQADV 4X9M HIS A -25 UNP P75063 EXPRESSION TAG SEQADV 4X9M HIS A -24 UNP P75063 EXPRESSION TAG SEQADV 4X9M SER A -23 UNP P75063 EXPRESSION TAG SEQADV 4X9M SER A -22 UNP P75063 EXPRESSION TAG SEQADV 4X9M GLY A -21 UNP P75063 EXPRESSION TAG SEQADV 4X9M LEU A -20 UNP P75063 EXPRESSION TAG SEQADV 4X9M VAL A -19 UNP P75063 EXPRESSION TAG SEQADV 4X9M PRO A -18 UNP P75063 EXPRESSION TAG SEQADV 4X9M ARG A -17 UNP P75063 EXPRESSION TAG SEQADV 4X9M GLY A -16 UNP P75063 EXPRESSION TAG SEQADV 4X9M SER A -15 UNP P75063 EXPRESSION TAG SEQADV 4X9M HIS A -14 UNP P75063 EXPRESSION TAG SEQADV 4X9M MET A -13 UNP P75063 EXPRESSION TAG SEQADV 4X9M ALA A -12 UNP P75063 EXPRESSION TAG SEQADV 4X9M SER A -11 UNP P75063 EXPRESSION TAG SEQADV 4X9M MET A -10 UNP P75063 EXPRESSION TAG SEQADV 4X9M THR A -9 UNP P75063 EXPRESSION TAG SEQADV 4X9M GLY A -8 UNP P75063 EXPRESSION TAG SEQADV 4X9M GLY A -7 UNP P75063 EXPRESSION TAG SEQADV 4X9M GLN A -6 UNP P75063 EXPRESSION TAG SEQADV 4X9M GLN A -5 UNP P75063 EXPRESSION TAG SEQADV 4X9M MET A -4 UNP P75063 EXPRESSION TAG SEQADV 4X9M GLY A -3 UNP P75063 EXPRESSION TAG SEQADV 4X9M ARG A -2 UNP P75063 EXPRESSION TAG SEQADV 4X9M GLY A -1 UNP P75063 EXPRESSION TAG SEQADV 4X9M 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 HET G3P A 403 10 HETNAM FAD FLAVIN-ADENINE DINUCLEOTIDE HETNAM NI NICKEL (II) ION HETNAM G3P SN-GLYCEROL-3-PHOSPHATE FORMUL 2 FAD C27 H33 N9 O15 P2 FORMUL 3 NI NI 2+ FORMUL 4 G3P C3 H9 O6 P FORMUL 5 HOH *201(H2 O) HELIX 1 AA1 GLY A 12 SER A 23 1 12 HELIX 2 AA2 LYS A 60 THR A 76 1 17 HELIX 3 AA3 THR A 76 ARG A 80 1 5 HELIX 4 AA4 ASN A 96 ASN A 113 1 18 HELIX 5 AA5 ASN A 116 GLU A 118 5 3 HELIX 6 AA6 LYS A 125 GLU A 132 1 8 HELIX 7 AA7 ASP A 152 ASN A 167 1 16 HELIX 8 AA8 ALA A 209 HIS A 211 5 3 HELIX 9 AA9 TYR A 212 ALA A 220 1 9 HELIX 10 AB1 VAL A 252 GLY A 257 1 6 HELIX 11 AB2 ASP A 281 THR A 285 5 5 HELIX 12 AB3 ASP A 291 VAL A 304 1 14 HELIX 13 AB4 PRO A 349 LEU A 365 1 17 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 CYS A 172 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 VAL A 9 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 SER A 181 O LEU A 189 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 CYS A 172 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 VAL A 9 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 LEU A 271 N SER A 263 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 LEU A 271 N SER A 263 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 2.42 LINK NE2 HIS A 59 NI NI A 402 1555 1555 2.05 LINK NH2 ARG A 320 O1P G3P A 403 1555 1555 1.38 LINK NH2 ARG A 320 P G3P A 403 1555 1555 1.60 LINK NH2 ARG A 320 O3P G3P A 403 1555 1555 1.48 LINK NI NI A 402 O HOH A 541 1555 1555 2.21 LINK NE2 HIS A 59 NI NI A 402 1555 6555 2.05 LINK NI NI A 402 O HOH A 541 1555 6555 2.21 CISPEP 1 GLY A 273 PRO A 274 0 10.33 CISPEP 2 SER A 348 PRO A 349 0 9.64 SITE 1 AC1 37 GLY A 10 GLY A 12 VAL A 13 ILE A 14 SITE 2 AC1 37 GLU A 33 LYS A 34 HIS A 35 GLU A 41 SITE 3 AC1 37 THR A 42 SER A 43 ALA A 45 ASN A 46 SITE 4 AC1 37 SER A 47 GLY A 48 VAL A 49 HIS A 51 SITE 5 AC1 37 THR A 175 GLU A 176 VAL A 177 ALA A 208 SITE 6 AC1 37 ALA A 209 GLY A 210 TYR A 212 TYR A 234 SITE 7 AC1 37 SER A 319 ARG A 320 MET A 346 LYS A 347 SITE 8 AC1 37 SER A 348 PRO A 349 GLY A 350 LEU A 351 SITE 9 AC1 37 THR A 352 HOH A 550 HOH A 556 HOH A 558 SITE 10 AC1 37 HOH A 563 SITE 1 AC2 2 HIS A 59 HOH A 541 CRYST1 111.590 111.590 111.590 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 0.008961 0.000000 0.000000 0.00000 SCALE2 0.000000 0.008961 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008961 0.00000 MASTER 423 0 3 13 33 0 11 6 0 0 0 33 END