HEADER OXIDOREDUCTASE 02-NOV-08 2W2K TITLE CRYSTAL STRUCTURE OF THE APO FORMS OF RHODOTORULA GRAMINIS D- TITLE 2 MANDELATE DEHYDROGENASE AT 1.8A. COMPND MOL_ID: 1; COMPND 2 MOLECULE: D-MANDELATE DEHYDROGENASE; COMPND 3 CHAIN: A; COMPND 4 MOL_ID: 2; COMPND 5 MOLECULE: D-MANDELATE DEHYDROGENASE; COMPND 6 CHAIN: B; COMPND 7 OTHER_DETAILS: THE PROTEIN IS BIOLOGICALLY ACTIVE AND CRYSTALLIZES AS COMPND 8 A DIMER SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RHODOTORULA GRAMINIS; SOURCE 3 ORGANISM_TAXID: 29898; SOURCE 4 STRAIN: KGX39; SOURCE 5 MOL_ID: 2; SOURCE 6 ORGANISM_SCIENTIFIC: RHODOTORULA GRAMINIS; SOURCE 7 ORGANISM_TAXID: 29898; SOURCE 8 STRAIN: KGX39; SOURCE 9 OTHER_DETAILS: C.A.FEWSON KEYWDS MANDELATE DEHYDROGENASE, 2-HYDROXYACID DEHYDROGENASE, OXIDOREDUCTASE EXPDTA X-RAY DIFFRACTION AUTHOR S.G.VACHIERI,A.R.COLE,C.BAGNERIS,D.P.BAKER,C.A.FEWSON,A.K.BASAK REVDAT 2 13-DEC-23 2W2K 1 REMARK REVDAT 1 17-NOV-09 2W2K 0 JRNL AUTH S.G.VACHIERI,A.R.COLE,C.BAGNERIS,D.P.BAKER,C.A.FEWSON, JRNL AUTH 2 A.K.BASAK JRNL TITL CRYSTAL STRUCTURE OF THE APO AND HOLO FORMS OF RHODOTORULA JRNL TITL 2 GRAMINIS D(-)-MANDELATE DEHYDROGENASE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.85 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 1.85 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.96 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 56812 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) : 0.156 REMARK 3 R VALUE (WORKING SET) : 0.154 REMARK 3 FREE R VALUE : 0.199 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3020 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) : 1.85 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.90 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3659 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.1750 REMARK 3 BIN FREE R VALUE SET COUNT : 176 REMARK 3 BIN FREE R VALUE : 0.2480 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5304 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 741 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 15.12 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.06000 REMARK 3 B22 (A**2) : -0.07000 REMARK 3 B33 (A**2) : -0.01000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.11000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.123 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.122 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.071 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.279 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.959 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.933 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5344 ; 0.019 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7259 ; 1.329 ; 1.959 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 691 ; 6.030 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 225 ;35.326 ;23.600 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 856 ;12.019 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 35 ;15.330 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 831 ; 0.093 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4049 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1857 ; 0.184 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3494 ; 0.285 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 352 ; 0.128 ; 0.200 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): 30 ; 0.127 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 31 ; 0.117 ; 0.200 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): 3628 ; 2.068 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5472 ; 2.624 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2052 ; 4.154 ; 4.500 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1785 ; 5.349 ; 6.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL 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 : 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. PRO 2 A AND PRO 2 B WERE MODELLED AS ALA DUE TO REMARK 3 DISORDERED SIDE CHAIN DENSITY MET 1 A, MET 1 B, SER 346 B WERE REMARK 3 NOT MODELLED DUE TO DISORDERED DENSITY REMARK 4 REMARK 4 2W2K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 02-NOV-08. REMARK 100 THE DEPOSITION ID IS D_1290037229. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SRS REMARK 200 BEAMLINE : PX9.6 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.933 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 59834 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 29.800 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 2.400 REMARK 200 R MERGE (I) : 0.05000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 0.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.85 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.30 REMARK 200 R MERGE FOR SHELL (I) : 0.09000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 9.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1MX3 REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 50.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.49 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM MES-NAOH PH 6.0, 200 MM NACL, REMARK 280 20% PEG-MME5K, 1% DIOXANE, 1MM DTT. REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 40.53550 REMARK 290 SMTRY3 2 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: 5410 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28620 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.8 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 1 REMARK 465 ALA A 347 REMARK 465 ALA A 348 REMARK 465 MET B 1 REMARK 465 SER B 346 REMARK 465 ALA B 347 REMARK 465 ALA B 348 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 PRO A 2 CG CD REMARK 470 LEU A 233 CG CD1 CD2 REMARK 470 PRO B 2 CG CD REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ARG A 14 CD NE CZ NH1 NH2 REMARK 480 LYS A 41 CE NZ REMARK 480 ARG A 45 NH1 NH2 REMARK 480 LYS A 47 NZ REMARK 480 ARG A 48 CD NE CZ NH1 NH2 REMARK 480 LYS A 156 NZ REMARK 480 ARG A 162 NH1 NH2 REMARK 480 LYS A 176 NZ REMARK 480 LYS A 189 NZ REMARK 480 ALA A 200 CB REMARK 480 GLU A 201 CG CD OE1 OE2 REMARK 480 LYS A 204 CG CD CE NZ REMARK 480 LYS A 232 CB CG CD CE NZ REMARK 480 ARG A 257 CD NE CZ NH1 NH2 REMARK 480 LYS A 271 NZ REMARK 480 LYS A 291 CG CD CE NZ REMARK 480 GLU A 295 CD OE1 OE2 REMARK 480 LYS A 340 CD CE NZ REMARK 480 ARG B 45 NE CZ NH1 NH2 REMARK 480 LYS B 47 CE NZ REMARK 480 ARG B 48 CD NE CZ NH1 NH2 REMARK 480 ASP B 92 CG OD1 OD2 REMARK 480 GLU B 145 CD OE1 OE2 REMARK 480 LYS B 156 CE NZ REMARK 480 ARG B 162 CZ NH1 NH2 REMARK 480 LYS B 189 NZ REMARK 480 LYS B 204 CG CD CE NZ REMARK 480 LYS B 232 CD CE NZ REMARK 480 GLU B 240 CD OE1 OE2 REMARK 480 LYS B 271 CE NZ REMARK 480 GLU B 295 CD OE1 OE2 REMARK 480 LYS B 340 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 NH2 ARG B 45 O HOH B 2085 0.74 REMARK 500 CZ ARG B 45 O HOH B 2085 1.11 REMARK 500 NH1 ARG B 162 O HOH B 2230 1.62 REMARK 500 NH1 ARG B 45 O HOH B 2085 1.98 REMARK 500 OE2 GLU B 240 O HOH B 2296 2.08 REMARK 500 O HOH A 2050 O HOH A 2059 2.09 REMARK 500 OE2 GLU B 240 O HOH B 2295 2.13 REMARK 500 NH1 ARG A 14 O HOH A 2024 2.14 REMARK 500 NE ARG B 45 O HOH B 2085 2.14 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 ARG A 14 CG ARG A 14 CD 0.223 REMARK 500 LYS A 41 CD LYS A 41 CE -0.267 REMARK 500 LYS A 156 CE LYS A 156 NZ -0.454 REMARK 500 ARG A 162 CZ ARG A 162 NH1 0.096 REMARK 500 ARG A 162 CZ ARG A 162 NH2 0.607 REMARK 500 LYS A 176 CE LYS A 176 NZ -0.340 REMARK 500 LYS A 204 CB LYS A 204 CG -0.296 REMARK 500 LYS A 271 CE LYS A 271 NZ 0.159 REMARK 500 LYS A 291 CB LYS A 291 CG -0.211 REMARK 500 ARG B 48 CG ARG B 48 CD -0.213 REMARK 500 ASP B 92 CB ASP B 92 CG -0.740 REMARK 500 LYS B 189 CE LYS B 189 NZ -0.220 REMARK 500 GLU B 240 CG GLU B 240 CD -0.096 REMARK 500 GLU B 295 CG GLU B 295 CD -0.111 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 PRO A 2 N - CA - CB ANGL. DEV. = 7.6 DEGREES REMARK 500 ARG A 14 CB - CG - CD ANGL. DEV. = -18.0 DEGREES REMARK 500 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 5.1 DEGREES REMARK 500 ARG A 45 NE - CZ - NH2 ANGL. DEV. = -5.0 DEGREES REMARK 500 LYS A 156 CD - CE - NZ ANGL. DEV. = 21.8 DEGREES REMARK 500 ARG A 162 NH1 - CZ - NH2 ANGL. DEV. = -34.6 DEGREES REMARK 500 ARG A 162 NE - CZ - NH1 ANGL. DEV. = 23.9 DEGREES REMARK 500 LYS A 176 CD - CE - NZ ANGL. DEV. = 16.9 DEGREES REMARK 500 ALA A 200 CB - CA - C ANGL. DEV. = 11.4 DEGREES REMARK 500 ARG A 257 CB - CG - CD ANGL. DEV. = 16.8 DEGREES REMARK 500 LYS A 271 CD - CE - NZ ANGL. DEV. = -15.2 DEGREES REMARK 500 LYS A 291 CA - CB - CG ANGL. DEV. = 13.6 DEGREES REMARK 500 ASP B 92 CA - CB - CG ANGL. DEV. = 25.7 DEGREES REMARK 500 ASP B 92 CB - CG - OD2 ANGL. DEV. = 9.1 DEGREES REMARK 500 LYS B 156 CD - CE - NZ ANGL. DEV. = -15.0 DEGREES REMARK 500 ARG B 162 NE - CZ - NH2 ANGL. DEV. = -3.7 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 35 -70.35 -116.85 REMARK 500 PHE A 91 52.32 -149.20 REMARK 500 ASP A 239 -168.16 -123.07 REMARK 500 ALA A 256 -99.79 -88.97 REMARK 500 LEU B 16 73.93 -102.80 REMARK 500 THR B 35 -73.89 -114.92 REMARK 500 SER B 227 85.66 -150.51 REMARK 500 ALA B 256 -103.39 -84.47 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 162 0.09 SIDE CHAIN 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 B2005 DISTANCE = 6.95 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2W2L RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF THE HOLO FORMS OF RHODOTORULA GRAMINIS D- REMARK 900 MANDELATE DEHYDROGENASE AT 2.5A. REMARK 999 REMARK 999 SEQUENCE REMARK 999 IMPORTANT SEQUENCE DISCREPANCIES EXIST WITH THE UNIPROT REMARK 999 ENTRY. THE AUTHOR OF THE ENTRY HAS BEEN INFORMED AND IS IN REMARK 999 THE PROCESS OF UPDATING THE ENTRY. THE ORIGINAL ENTRY IN REMARK 999 THE DATABANK SPECIFIED STARTING FROM RESIDUE 337 UNTIL REMARK 999 LAST RESIDUE, THE FOLLOWING SEQUENCE VRLCPNSLRPAFRAY, REMARK 999 INSTEAD THE STRUCTURE SHOWS THE FOLLOWING SEQUENCE REMARK 999 PAGKVFAPSS. THIS INFORMATION OBTAINED FROM THE STRUCTURE REMARK 999 WAS COMPARED WITH THE GENE GENOMIC SEQUENCE AND PROVED REMARK 999 THAT THE INITIAL INTRON AND EXON ASSIGNMENT WAS INCORRECT. DBREF 2W2K A 1 348 UNP Q7LLW9 Q7LLW9_RHOGR 1 348 DBREF 2W2K B 1 348 UNP Q7LLW9 Q7LLW9_RHOGR 1 348 SEQADV 2W2K ASN B 288 UNP Q7LLW9 GLN 288 CONFLICT SEQRES 1 A 348 MET PRO ARG PRO ARG VAL LEU LEU LEU GLY ASP PRO ALA SEQRES 2 A 348 ARG HIS LEU ASP ASP LEU TRP SER ASP PHE GLN GLN LYS SEQRES 3 A 348 PHE GLU VAL ILE PRO ALA ASN LEU THR THR HIS ASP GLY SEQRES 4 A 348 PHE LYS GLN ALA LEU ARG GLU LYS ARG TYR GLY ASP PHE SEQRES 5 A 348 GLU ALA ILE ILE LYS LEU ALA VAL GLU ASN GLY THR GLU SEQRES 6 A 348 SER TYR PRO TRP ASN ALA ASP LEU ILE SER HIS LEU PRO SEQRES 7 A 348 SER SER LEU LYS VAL PHE ALA ALA ALA GLY ALA GLY PHE SEQRES 8 A 348 ASP TRP LEU ASP LEU ASP ALA LEU ASN GLU ARG GLY VAL SEQRES 9 A 348 ALA PHE ALA ASN SER ARG GLY ALA GLY ASP THR ALA THR SEQRES 10 A 348 SER ASP LEU ALA LEU TYR LEU ILE LEU SER VAL PHE ARG SEQRES 11 A 348 LEU ALA SER TYR SER GLU ARG ALA ALA ARG THR GLY ASP SEQRES 12 A 348 PRO GLU THR PHE ASN ARG VAL HIS LEU GLU ILE GLY LYS SEQRES 13 A 348 SER ALA HIS ASN PRO ARG GLY HIS VAL LEU GLY ALA VAL SEQRES 14 A 348 GLY LEU GLY ALA ILE GLN LYS GLU ILE ALA ARG LYS ALA SEQRES 15 A 348 VAL HIS GLY LEU GLY MET LYS LEU VAL TYR TYR ASP VAL SEQRES 16 A 348 ALA PRO ALA ASP ALA GLU THR GLU LYS ALA LEU GLY ALA SEQRES 17 A 348 GLU ARG VAL ASP SER LEU GLU GLU LEU ALA ARG ARG SER SEQRES 18 A 348 ASP CYS VAL SER VAL SER VAL PRO TYR MET LYS LEU THR SEQRES 19 A 348 HIS HIS LEU ILE ASP GLU ALA PHE PHE ALA ALA MET LYS SEQRES 20 A 348 PRO GLY SER ARG ILE VAL ASN THR ALA ARG GLY PRO VAL SEQRES 21 A 348 ILE SER GLN ASP ALA LEU ILE ALA ALA LEU LYS SER GLY SEQRES 22 A 348 LYS LEU LEU SER ALA GLY LEU ASP VAL HIS GLU PHE GLU SEQRES 23 A 348 PRO GLN VAL SER LYS GLU LEU ILE GLU MET LYS HIS VAL SEQRES 24 A 348 THR LEU THR THR HIS ILE GLY GLY VAL ALA ILE GLU THR SEQRES 25 A 348 PHE HIS GLU PHE GLU ARG LEU THR MET THR ASN ILE ASP SEQRES 26 A 348 ARG PHE LEU LEU GLN GLY LYS PRO LEU LEU THR PRO ALA SEQRES 27 A 348 GLY LYS VAL PHE ALA PRO SER SER ALA ALA SEQRES 1 B 348 MET PRO ARG PRO ARG VAL LEU LEU LEU GLY ASP PRO ALA SEQRES 2 B 348 ARG HIS LEU ASP ASP LEU TRP SER ASP PHE GLN GLN LYS SEQRES 3 B 348 PHE GLU VAL ILE PRO ALA ASN LEU THR THR HIS ASP GLY SEQRES 4 B 348 PHE LYS GLN ALA LEU ARG GLU LYS ARG TYR GLY ASP PHE SEQRES 5 B 348 GLU ALA ILE ILE LYS LEU ALA VAL GLU ASN GLY THR GLU SEQRES 6 B 348 SER TYR PRO TRP ASN ALA ASP LEU ILE SER HIS LEU PRO SEQRES 7 B 348 SER SER LEU LYS VAL PHE ALA ALA ALA GLY ALA GLY PHE SEQRES 8 B 348 ASP TRP LEU ASP LEU ASP ALA LEU ASN GLU ARG GLY VAL SEQRES 9 B 348 ALA PHE ALA ASN SER ARG GLY ALA GLY ASP THR ALA THR SEQRES 10 B 348 SER ASP LEU ALA LEU TYR LEU ILE LEU SER VAL PHE ARG SEQRES 11 B 348 LEU ALA SER TYR SER GLU ARG ALA ALA ARG THR GLY ASP SEQRES 12 B 348 PRO GLU THR PHE ASN ARG VAL HIS LEU GLU ILE GLY LYS SEQRES 13 B 348 SER ALA HIS ASN PRO ARG GLY HIS VAL LEU GLY ALA VAL SEQRES 14 B 348 GLY LEU GLY ALA ILE GLN LYS GLU ILE ALA ARG LYS ALA SEQRES 15 B 348 VAL HIS GLY LEU GLY MET LYS LEU VAL TYR TYR ASP VAL SEQRES 16 B 348 ALA PRO ALA ASP ALA GLU THR GLU LYS ALA LEU GLY ALA SEQRES 17 B 348 GLU ARG VAL ASP SER LEU GLU GLU LEU ALA ARG ARG SER SEQRES 18 B 348 ASP CYS VAL SER VAL SER VAL PRO TYR MET LYS LEU THR SEQRES 19 B 348 HIS HIS LEU ILE ASP GLU ALA PHE PHE ALA ALA MET LYS SEQRES 20 B 348 PRO GLY SER ARG ILE VAL ASN THR ALA ARG GLY PRO VAL SEQRES 21 B 348 ILE SER GLN ASP ALA LEU ILE ALA ALA LEU LYS SER GLY SEQRES 22 B 348 LYS LEU LEU SER ALA GLY LEU ASP VAL HIS GLU PHE GLU SEQRES 23 B 348 PRO ASN VAL SER LYS GLU LEU ILE GLU MET LYS HIS VAL SEQRES 24 B 348 THR LEU THR THR HIS ILE GLY GLY VAL ALA ILE GLU THR SEQRES 25 B 348 PHE HIS GLU PHE GLU ARG LEU THR MET THR ASN ILE ASP SEQRES 26 B 348 ARG PHE LEU LEU GLN GLY LYS PRO LEU LEU THR PRO ALA SEQRES 27 B 348 GLY LYS VAL PHE ALA PRO SER SER ALA ALA FORMUL 3 HOH *741(H2 O) HELIX 1 1 LEU A 16 PHE A 27 1 12 HELIX 2 2 THR A 36 GLU A 46 1 11 HELIX 3 3 GLY A 63 TYR A 67 5 5 HELIX 4 4 ASN A 70 SER A 75 1 6 HELIX 5 5 ASP A 95 ARG A 102 1 8 HELIX 6 6 GLY A 113 LEU A 131 1 19 HELIX 7 7 LEU A 131 ARG A 140 1 10 HELIX 8 8 ASP A 143 LYS A 156 1 14 HELIX 9 9 GLY A 172 GLY A 185 1 14 HELIX 10 10 ASP A 199 GLY A 207 1 9 HELIX 11 11 SER A 213 SER A 221 1 9 HELIX 12 12 MET A 231 HIS A 235 5 5 HELIX 13 13 ASP A 239 MET A 246 1 8 HELIX 14 14 ARG A 257 VAL A 260 5 4 HELIX 15 15 SER A 262 SER A 272 1 11 HELIX 16 16 SER A 290 GLU A 295 1 6 HELIX 17 17 ALA A 309 GLN A 330 1 22 HELIX 18 18 LEU B 16 PHE B 27 1 12 HELIX 19 19 THR B 36 GLU B 46 1 11 HELIX 20 20 GLY B 63 TYR B 67 5 5 HELIX 21 21 ASN B 70 SER B 75 1 6 HELIX 22 22 ASP B 95 ARG B 102 1 8 HELIX 23 23 GLY B 113 LEU B 131 1 19 HELIX 24 24 LEU B 131 ARG B 140 1 10 HELIX 25 25 ASP B 143 GLY B 155 1 13 HELIX 26 26 GLY B 172 GLY B 185 1 14 HELIX 27 27 ASP B 199 GLY B 207 1 9 HELIX 28 28 SER B 213 SER B 221 1 9 HELIX 29 29 MET B 231 HIS B 235 5 5 HELIX 30 30 ASP B 239 MET B 246 1 8 HELIX 31 31 ARG B 257 VAL B 260 5 4 HELIX 32 32 SER B 262 SER B 272 1 11 HELIX 33 33 SER B 290 GLU B 295 1 6 HELIX 34 34 ALA B 309 GLN B 330 1 22 SHEET 1 AA 5 GLU A 28 PRO A 31 0 SHEET 2 AA 5 ARG A 5 LEU A 8 1 O VAL A 6 N ILE A 30 SHEET 3 AA 5 ALA A 54 LYS A 57 1 O ALA A 54 N LEU A 7 SHEET 4 AA 5 VAL A 83 ALA A 86 1 O VAL A 83 N ILE A 55 SHEET 5 AA 5 ALA A 105 ALA A 107 1 O ALA A 105 N PHE A 84 SHEET 1 AB 7 GLU A 209 ARG A 210 0 SHEET 2 AB 7 LYS A 189 TYR A 193 1 O LEU A 190 N GLU A 209 SHEET 3 AB 7 VAL A 165 VAL A 169 1 O LEU A 166 N VAL A 191 SHEET 4 AB 7 CYS A 223 VAL A 226 1 O CYS A 223 N GLY A 167 SHEET 5 AB 7 SER A 250 ASN A 254 1 O ARG A 251 N VAL A 224 SHEET 6 AB 7 LEU A 275 LEU A 280 1 N LEU A 276 O SER A 250 SHEET 7 AB 7 VAL A 299 LEU A 301 1 O THR A 300 N LEU A 280 SHEET 1 BA 5 GLU B 28 PRO B 31 0 SHEET 2 BA 5 ARG B 5 LEU B 8 1 O VAL B 6 N ILE B 30 SHEET 3 BA 5 ALA B 54 LYS B 57 1 O ALA B 54 N LEU B 7 SHEET 4 BA 5 VAL B 83 ALA B 86 1 O VAL B 83 N ILE B 55 SHEET 5 BA 5 ALA B 105 ALA B 107 1 O ALA B 105 N PHE B 84 SHEET 1 BB 7 GLU B 209 ARG B 210 0 SHEET 2 BB 7 LYS B 189 TYR B 193 1 O LEU B 190 N GLU B 209 SHEET 3 BB 7 VAL B 165 VAL B 169 1 O LEU B 166 N VAL B 191 SHEET 4 BB 7 CYS B 223 VAL B 226 1 O CYS B 223 N GLY B 167 SHEET 5 BB 7 SER B 250 ASN B 254 1 O ARG B 251 N VAL B 224 SHEET 6 BB 7 LEU B 275 LEU B 280 1 N LEU B 276 O SER B 250 SHEET 7 BB 7 VAL B 299 LEU B 301 1 O THR B 300 N LEU B 280 CISPEP 1 TYR A 67 PRO A 68 0 0.33 CISPEP 2 GLU A 286 PRO A 287 0 8.77 CISPEP 3 TYR B 67 PRO B 68 0 -4.23 CISPEP 4 GLU B 286 PRO B 287 0 7.84 CRYST1 50.030 81.071 93.955 90.00 96.27 90.00 P 1 21 1 2 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 0.019988 0.000000 0.002196 0.00000 SCALE2 0.000000 0.012335 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010707 0.00000