HEADER OXIDOREDUCTASE 14-NOV-24 9KL6 TITLE CRYSTAL STRUCTURE OF NADP-SPECIFIC GLUTAMATE DEHYDROGENASE GDH1 FROM TITLE 2 SCHIZOSACCHAROMYCES POMBE IN COMPLEX WITH ALPHA-IMINOGLUTARATE AND TITLE 3 NADP+ COMPND MOL_ID: 1; COMPND 2 MOLECULE: NADP-SPECIFIC GLUTAMATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: NADP-GDH,NADP-DEPENDENT GLUTAMATE DEHYDROGENASE; COMPND 5 EC: 1.4.1.4; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCHIZOSACCHAROMYCES POMBE; SOURCE 3 ORGANISM_COMMON: FISSION YEAST; SOURCE 4 ORGANISM_TAXID: 4896; SOURCE 5 GENE: GDH1, SPCC622.12C; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS GLUTAMATE DEHYDROGENASE, NADP, ROSSMANN FOLD, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR T.TOMITA,A.YOSHIDA,M.NISHIYAMA REVDAT 3 04-MAR-26 9KL6 1 REMARK REVDAT 2 06-AUG-25 9KL6 1 JRNL REVDAT 1 30-JUL-25 9KL6 0 JRNL AUTH Y.F.WANG,T.TOMITA,A.YOSHIDA,S.KOSONO,M.NISHIYAMA JRNL TITL PHOSPHORYLATION-MEDIATED REGULATION OF THE NADPH-DEPENDENT JRNL TITL 2 GLUTAMATE DEHYDROGENASE, SPGDH1, FROM SCHIZOSACCHAROMYCES JRNL TITL 3 POMBE. JRNL REF J.BIOL.CHEM. V. 301 10422 2025 JRNL REFN ESSN 1083-351X JRNL PMID 40578557 JRNL DOI 10.1016/J.JBC.2025.110422 REMARK 2 REMARK 2 RESOLUTION. 1.45 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0419 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) : 1.45 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 88100 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) : 0.181 REMARK 3 R VALUE (WORKING SET) : 0.179 REMARK 3 FREE R VALUE : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4666 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) : 1.45 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.49 REMARK 3 REFLECTION IN BIN (WORKING SET) : 6329 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.01 REMARK 3 BIN R VALUE (WORKING SET) : 0.2310 REMARK 3 BIN FREE R VALUE SET COUNT : 340 REMARK 3 BIN FREE R VALUE : 0.2440 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3414 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 75 REMARK 3 SOLVENT ATOMS : 417 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 21.65 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 2.46000 REMARK 3 B22 (A**2) : 2.46000 REMARK 3 B33 (A**2) : -7.99000 REMARK 3 B12 (A**2) : 1.23000 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): 0.072 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.065 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.062 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.812 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.944 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3593 ; 0.010 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 3375 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 4857 ; 1.782 ; 1.818 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7785 ; 0.648 ; 1.756 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 454 ; 6.086 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 23 ; 7.963 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 602 ;12.061 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 522 ; 0.102 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4263 ; 0.011 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 822 ; 0.001 ; 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): 1810 ; 5.980 ; 2.204 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1810 ; 5.978 ; 2.204 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2266 ; 7.279 ; 3.974 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2267 ; 7.279 ; 3.974 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1783 ; 7.419 ; 2.438 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1777 ; 7.390 ; 2.435 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2586 ; 9.829 ; 4.388 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4157 ;13.030 ;22.530 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4050 ;12.084 ;21.530 REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): 6968 ; 4.656 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 9KL6 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-NOV-24. REMARK 100 THE DEPOSITION ID IS D_1300053510. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-NOV-19 REMARK 200 TEMPERATURE (KELVIN) : 95 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : PHOTON FACTORY REMARK 200 BEAMLINE : AR-NW12A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 S 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 92864 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.450 REMARK 200 RESOLUTION RANGE LOW (A) : 46.990 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 19.00 REMARK 200 R MERGE (I) : 0.07600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.45 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 15.60 REMARK 200 R MERGE FOR SHELL (I) : 0.93100 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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: 5GUD REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.75 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.50 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M HEPES-NAOH, PH 7.5, 1.6M AMMONIUM REMARK 280 SULFATE, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-Z+1/2 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 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 94.12900 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 94.12900 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 94.12900 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 94.12900 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 94.12900 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 94.12900 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: HEXAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: HEXAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 33570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 81140 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -183.0 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 -0.500000 -0.866025 0.000000 -48.48250 REMARK 350 BIOMT2 2 0.866025 -0.500000 0.000000 -83.97415 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 3 -0.500000 0.866025 0.000000 48.48250 REMARK 350 BIOMT2 3 -0.866025 -0.500000 0.000000 -83.97415 REMARK 350 BIOMT3 3 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 4 0.500000 -0.866025 0.000000 -48.48250 REMARK 350 BIOMT2 4 -0.866025 -0.500000 0.000000 -83.97415 REMARK 350 BIOMT3 4 0.000000 0.000000 -1.000000 94.12900 REMARK 350 BIOMT1 5 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 5 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 5 0.000000 0.000000 -1.000000 94.12900 REMARK 350 BIOMT1 6 0.500000 0.866025 0.000000 48.48250 REMARK 350 BIOMT2 6 0.866025 -0.500000 0.000000 -83.97415 REMARK 350 BIOMT3 6 0.000000 0.000000 -1.000000 94.12900 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 618 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 800 LIES ON A SPECIAL POSITION. REMARK 375 HOH A1002 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 -20 REMARK 465 LYS A -19 REMARK 465 HIS A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 GLY A -10 REMARK 465 GLY A -9 REMARK 465 LEU A -8 REMARK 465 VAL A -7 REMARK 465 PRO A -6 REMARK 465 ARG A -5 REMARK 465 GLY A -4 REMARK 465 SER A -3 REMARK 465 HIS A -2 REMARK 465 GLY A -1 REMARK 465 GLY A 0 REMARK 465 SER A 1 REMARK 465 SER A 2 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 THR A 3 OG1 CG2 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 A 44 NE - CZ - NH2 ANGL. DEV. = -4.6 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 THR A 147 -57.88 -123.65 REMARK 500 ALA A 151 -169.48 -170.56 REMARK 500 ASP A 153 -149.01 -116.12 REMARK 500 ILE A 191 -13.02 78.41 REMARK 500 SER A 228 23.08 -155.97 REMARK 500 HIS A 292 -157.84 -106.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 141 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL DBREF 9KL6 A 2 451 UNP P78804 DHE4_SCHPO 2 451 SEQADV 9KL6 MET A -20 UNP P78804 INITIATING METHIONINE SEQADV 9KL6 LYS A -19 UNP P78804 EXPRESSION TAG SEQADV 9KL6 HIS A -18 UNP P78804 EXPRESSION TAG SEQADV 9KL6 HIS A -17 UNP P78804 EXPRESSION TAG SEQADV 9KL6 HIS A -16 UNP P78804 EXPRESSION TAG SEQADV 9KL6 HIS A -15 UNP P78804 EXPRESSION TAG SEQADV 9KL6 HIS A -14 UNP P78804 EXPRESSION TAG SEQADV 9KL6 HIS A -13 UNP P78804 EXPRESSION TAG SEQADV 9KL6 HIS A -12 UNP P78804 EXPRESSION TAG SEQADV 9KL6 HIS A -11 UNP P78804 EXPRESSION TAG SEQADV 9KL6 GLY A -10 UNP P78804 EXPRESSION TAG SEQADV 9KL6 GLY A -9 UNP P78804 EXPRESSION TAG SEQADV 9KL6 LEU A -8 UNP P78804 EXPRESSION TAG SEQADV 9KL6 VAL A -7 UNP P78804 EXPRESSION TAG SEQADV 9KL6 PRO A -6 UNP P78804 EXPRESSION TAG SEQADV 9KL6 ARG A -5 UNP P78804 EXPRESSION TAG SEQADV 9KL6 GLY A -4 UNP P78804 EXPRESSION TAG SEQADV 9KL6 SER A -3 UNP P78804 EXPRESSION TAG SEQADV 9KL6 HIS A -2 UNP P78804 EXPRESSION TAG SEQADV 9KL6 GLY A -1 UNP P78804 EXPRESSION TAG SEQADV 9KL6 GLY A 0 UNP P78804 EXPRESSION TAG SEQADV 9KL6 SER A 1 UNP P78804 EXPRESSION TAG SEQRES 1 A 472 MET LYS HIS HIS HIS HIS HIS HIS HIS HIS GLY GLY LEU SEQRES 2 A 472 VAL PRO ARG GLY SER HIS GLY GLY SER SER THR PRO TYR SEQRES 3 A 472 GLU PRO GLU PHE GLN GLN ALA TYR LYS GLU ILE VAL GLY SEQRES 4 A 472 SER ILE GLU SER SER LYS LEU PHE GLU VAL HIS PRO GLU SEQRES 5 A 472 LEU LYS ARG VAL LEU PRO ILE ILE SER ILE PRO GLU ARG SEQRES 6 A 472 VAL LEU GLU PHE ARG VAL THR TRP GLU ASP ASP LYS GLY SEQRES 7 A 472 ASN CYS ARG VAL ASN THR GLY TYR ARG VAL GLN PHE ASN SEQRES 8 A 472 SER ALA LEU GLY PRO TYR LYS GLY GLY LEU ARG PHE HIS SEQRES 9 A 472 PRO SER VAL ASN LEU SER ILE LEU LYS PHE LEU GLY PHE SEQRES 10 A 472 GLU GLN ILE PHE LYS ASN ALA LEU THR GLY LEU PRO MET SEQRES 11 A 472 GLY GLY GLY LYS GLY GLY SER ASP PHE ASP PRO LYS GLY SEQRES 12 A 472 LYS SER ASP ASN GLU ILE ARG ARG PHE SER GLN ALA PHE SEQRES 13 A 472 MET ARG GLN LEU PHE ARG TYR ILE GLY PRO GLN THR ASP SEQRES 14 A 472 VAL PRO ALA GLY ASP ILE GLY VAL THR GLY PHE VAL VAL SEQRES 15 A 472 MET HIS MET PHE GLY GLU TYR LYS ARG LEU ARG ASN GLU SEQRES 16 A 472 TYR SER GLY VAL VAL THR GLY LYS HIS MET LEU THR GLY SEQRES 17 A 472 GLY SER ASN ILE ARG PRO GLU ALA THR GLY TYR GLY VAL SEQRES 18 A 472 VAL TYR TYR VAL LYS HIS MET ILE GLU HIS ARG THR LYS SEQRES 19 A 472 GLY ALA GLU THR LEU LYS GLY LYS ARG VAL ALA ILE SER SEQRES 20 A 472 GLY SER GLY ASN VAL ALA GLN TYR ALA ALA LEU LYS CYS SEQRES 21 A 472 ILE GLN GLU GLY ALA ILE VAL LYS SER ILE SER ASP SER SEQRES 22 A 472 LYS GLY VAL LEU ILE ALA LYS THR ALA GLU GLY LEU VAL SEQRES 23 A 472 PRO GLU GLU ILE HIS GLU ILE MET ALA LEU LYS GLU LYS SEQRES 24 A 472 ARG ALA SER ILE ALA ASP SER ALA SER LEU CYS LYS LYS SEQRES 25 A 472 HIS HIS TYR ILE ALA GLY ALA ARG PRO TRP THR ASN VAL SEQRES 26 A 472 GLY GLU ILE ASP ILE ALA LEU PRO CYS ALA THR GLN ASN SEQRES 27 A 472 GLU VAL SER GLY GLU GLU ALA ALA ALA LEU ILE LYS GLN SEQRES 28 A 472 GLY CYS ARG TYR VAL ALA GLU GLY SER ASN MET GLY SER SEQRES 29 A 472 SER ALA GLU ALA VAL GLU VAL PHE GLU LYS SER ARG ALA SEQRES 30 A 472 SER GLY GLU GLY CYS TRP LEU ALA PRO GLY LYS ALA ALA SEQRES 31 A 472 ASN ALA GLY GLY VAL ALA VAL SER GLY LEU GLU MET ALA SEQRES 32 A 472 GLN ASN ALA GLN PHE SER THR TRP THR HIS ALA GLU VAL SEQRES 33 A 472 ASP ALA LYS LEU ALA GLY ILE MET GLN ASN ILE PHE GLU SEQRES 34 A 472 GLN SER THR ASP VAL ALA SER LYS TYR CYS ASP SER GLY SEQRES 35 A 472 SER ASN ASN ILE PRO SER LEU VAL ASP GLY ALA ASN ILE SEQRES 36 A 472 ALA GLY PHE LEU LYS VAL ALA THR ALA MET GLN ALA VAL SEQRES 37 A 472 GLY ASP TRP TRP HET NAP A 501 48 HET SO4 A 502 5 HET 2IT A 503 10 HET GOL A 504 6 HET GOL A 505 6 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM SO4 SULFATE ION HETNAM 2IT (2Z)-2-IMINOPENTANEDIOIC ACID HETNAM GOL GLYCEROL HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 SO4 O4 S 2- FORMUL 4 2IT C5 H7 N O4 FORMUL 5 GOL 2(C3 H8 O3) FORMUL 7 HOH *417(H2 O) HELIX 1 AA1 GLU A 6 SER A 22 1 17 HELIX 2 AA2 LYS A 24 HIS A 29 1 6 HELIX 3 AA3 PRO A 30 ARG A 34 5 5 HELIX 4 AA4 VAL A 35 SER A 40 1 6 HELIX 5 AA5 ASN A 87 GLY A 106 1 20 HELIX 6 AA6 SER A 124 PHE A 140 1 17 HELIX 7 AA7 ARG A 141 ILE A 143 5 3 HELIX 8 AA8 THR A 157 ASN A 173 1 17 HELIX 9 AA9 ILE A 191 THR A 212 1 22 HELIX 10 AB1 GLY A 229 GLU A 242 1 14 HELIX 11 AB2 VAL A 265 LYS A 278 1 14 HELIX 12 AB3 SER A 281 ASP A 284 5 4 HELIX 13 AB4 SER A 285 HIS A 292 1 8 HELIX 14 AB5 SER A 320 GLN A 330 1 11 HELIX 15 AB6 SER A 344 GLY A 358 1 15 HELIX 16 AB7 PRO A 365 ASN A 370 1 6 HELIX 17 AB8 ALA A 371 PHE A 387 1 17 HELIX 18 AB9 THR A 391 CYS A 418 1 28 HELIX 19 AC1 SER A 427 VAL A 447 1 21 SHEET 1 AA1 4 ARG A 44 GLU A 53 0 SHEET 2 AA1 4 CYS A 59 ASN A 70 -1 O ARG A 60 N TRP A 52 SHEET 3 AA1 4 GLY A 111 SER A 116 -1 O LYS A 113 N VAL A 67 SHEET 4 AA1 4 LEU A 80 PHE A 82 1 N ARG A 81 O SER A 116 SHEET 1 AA2 2 TYR A 76 LYS A 77 0 SHEET 2 AA2 2 ASP A 148 VAL A 149 1 O VAL A 149 N TYR A 76 SHEET 1 AA3 7 HIS A 293 ALA A 296 0 SHEET 2 AA3 7 GLY A 254 ILE A 257 -1 N ILE A 257 O HIS A 293 SHEET 3 AA3 7 ILE A 245 SER A 250 -1 N ILE A 249 O LEU A 256 SHEET 4 AA3 7 ARG A 222 ILE A 225 1 N VAL A 223 O ILE A 245 SHEET 5 AA3 7 ILE A 309 LEU A 311 1 O LEU A 311 N ALA A 224 SHEET 6 AA3 7 TYR A 334 ALA A 336 1 O TYR A 334 N ALA A 310 SHEET 7 AA3 7 TRP A 362 ALA A 364 1 O TRP A 362 N VAL A 335 CRYST1 96.965 96.965 188.258 90.00 90.00 120.00 P 63 2 2 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 0.010313 0.005954 0.000000 0.00000 SCALE2 0.000000 0.011908 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005312 0.00000 CONECT 3447 3448 3449 3450 3469 CONECT 3448 3447 CONECT 3449 3447 CONECT 3450 3447 3451 CONECT 3451 3450 3452 CONECT 3452 3451 3453 3454 CONECT 3453 3452 3458 CONECT 3454 3452 3455 3456 CONECT 3455 3454 CONECT 3456 3454 3457 3458 CONECT 3457 3456 3491 CONECT 3458 3453 3456 3459 CONECT 3459 3458 3460 3468 CONECT 3460 3459 3461 CONECT 3461 3460 3462 CONECT 3462 3461 3463 3468 CONECT 3463 3462 3464 3465 CONECT 3464 3463 CONECT 3465 3463 3466 CONECT 3466 3465 3467 CONECT 3467 3466 3468 CONECT 3468 3459 3462 3467 CONECT 3469 3447 3470 CONECT 3470 3469 3471 3472 3473 CONECT 3471 3470 CONECT 3472 3470 CONECT 3473 3470 3474 CONECT 3474 3473 3475 CONECT 3475 3474 3476 3477 CONECT 3476 3475 3481 CONECT 3477 3475 3478 3479 CONECT 3478 3477 CONECT 3479 3477 3480 3481 CONECT 3480 3479 CONECT 3481 3476 3479 3482 CONECT 3482 3481 3483 3490 CONECT 3483 3482 3484 CONECT 3484 3483 3485 3488 CONECT 3485 3484 3486 3487 CONECT 3486 3485 CONECT 3487 3485 CONECT 3488 3484 3489 CONECT 3489 3488 3490 CONECT 3490 3482 3489 CONECT 3491 3457 3492 3493 3494 CONECT 3492 3491 CONECT 3493 3491 CONECT 3494 3491 CONECT 3495 3496 3497 3498 3499 CONECT 3496 3495 CONECT 3497 3495 CONECT 3498 3495 CONECT 3499 3495 CONECT 3500 3501 CONECT 3501 3500 3502 3503 CONECT 3502 3501 CONECT 3503 3501 3504 3505 CONECT 3504 3503 CONECT 3505 3503 3506 CONECT 3506 3505 3507 CONECT 3507 3506 3508 3509 CONECT 3508 3507 CONECT 3509 3507 CONECT 3510 3511 3512 CONECT 3511 3510 CONECT 3512 3510 3513 3514 CONECT 3513 3512 CONECT 3514 3512 3515 CONECT 3515 3514 CONECT 3516 3517 3518 CONECT 3517 3516 CONECT 3518 3516 3519 3520 CONECT 3519 3518 CONECT 3520 3518 3521 CONECT 3521 3520 MASTER 391 0 5 19 13 0 0 6 3906 1 75 37 END