HEADER BIOSYNTHETIC PROTEIN 25-APR-20 6YTZ TITLE CRYSTAL STRUCTURE OF MALUS DOMESTICA DOUBLE BOND REDUCTASE (MDDBR) IN TITLE 2 COMPLEX WITH NADPH COMPND MOL_ID: 1; COMPND 2 MOLECULE: DOUBLE BOND REDUCTASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MALUS DOMESTICA; SOURCE 3 ORGANISM_COMMON: APPLE; SOURCE 4 ORGANISM_TAXID: 3750; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHENYLPROPANOID PATHWAY, DOUBLE BOND REDUCTASE, MALUS DOMESTICA, KEYWDS 2 BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR R.CALIANDRO,I.POLSINELLI,N.DEMITRI,S.BENINI REVDAT 2 24-JAN-24 6YTZ 1 REMARK REVDAT 1 03-FEB-21 6YTZ 0 JRNL AUTH R.CALIANDRO,I.POLSINELLI,N.DEMITRI,F.MUSIANI,S.MARTENS, JRNL AUTH 2 S.BENINI JRNL TITL THE STRUCTURAL AND FUNCTIONAL CHARACTERIZATION OF MALUS JRNL TITL 2 DOMESTICA DOUBLE BOND REDUCTASE MDDBR PROVIDES INSIGHTS JRNL TITL 3 TOWARDS THE IDENTIFICATION OF ITS SUBSTRATES. JRNL REF INT.J.BIOL.MACROMOL. V. 171 89 2021 JRNL REFN ISSN 0141-8130 JRNL PMID 33412202 JRNL DOI 10.1016/J.IJBIOMAC.2020.12.190 REMARK 2 REMARK 2 RESOLUTION. 1.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0258 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) : 1.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.44 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 64352 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) : 0.124 REMARK 3 R VALUE (WORKING SET) : 0.122 REMARK 3 FREE R VALUE : 0.166 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3403 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) : 1.40 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.44 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4669 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.3830 REMARK 3 BIN FREE R VALUE SET COUNT : 284 REMARK 3 BIN FREE R VALUE : 0.3890 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2703 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 66 REMARK 3 SOLVENT ATOMS : 287 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.34 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.37000 REMARK 3 B22 (A**2) : -0.14000 REMARK 3 B33 (A**2) : 0.51000 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): 0.050 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.052 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.038 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.277 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.985 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.976 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2857 ; 0.016 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2713 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3875 ; 1.919 ; 1.645 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6305 ; 1.519 ; 1.575 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 361 ; 7.240 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 119 ;36.713 ;23.193 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 494 ;13.991 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 10 ;18.557 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 365 ; 0.116 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3158 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 575 ; 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): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL 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): 5566 ; 4.191 ; 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 U VALUES : REFINED INDIVIDUALLY REMARK 4 REMARK 4 6YTZ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 26-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292108254. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-DEC-18 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ELETTRA REMARK 200 BEAMLINE : 5.2R REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.00 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 67744 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.400 REMARK 200 RESOLUTION RANGE LOW (A) : 48.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.47 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.40 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.42 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: MOLREP REMARK 200 STARTING MODEL: 6YSB REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 44.23 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12.5% PEG 1000, 12.5% PEG 3350, 12.5% REMARK 280 MPD, 0.03 M MAGNESIUM CHLORIDE, 0.03 M CALCIUM CHLORIDE, 0.03 M REMARK 280 SODIUM CHLORIDE, 0.03 M SODIUM BROMIDE, 0.03 M SODIUM IODIDE IN REMARK 280 0.1 M MES/IMIDAZOLE PH 6.5., VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-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 -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 1.000000 0.000000 0.000000 34.27250 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.32250 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 72.69900 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 34.27250 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.32250 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 72.69900 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 34.27250 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 34.32250 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 72.69900 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 34.27250 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 34.32250 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 72.69900 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: 7070 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 28650 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -68.0 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 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 -68.64500 REMARK 350 BIOMT3 2 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 HOH A 564 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 752 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 783 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 785 LIES ON A SPECIAL POSITION. REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 701 O HOH A 721 1.35 REMARK 500 O HOH A 531 O HOH A 575 1.41 REMARK 500 O HOH A 517 O HOH A 679 1.57 REMARK 500 O HOH A 679 O HOH A 728 1.76 REMARK 500 NE2 GLN A 127 O HOH A 501 1.78 REMARK 500 OE2 GLU A 153 O HOH A 502 1.91 REMARK 500 O HOH A 621 O HOH A 680 1.92 REMARK 500 OD1 ASP A 217 O HOH A 503 2.00 REMARK 500 O HOH A 667 O HOH A 727 2.01 REMARK 500 O HOH A 639 O HOH A 706 2.16 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH A 501 O HOH A 721 7454 1.80 REMARK 500 CE MET A 285 CE MET A 285 2545 2.19 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 GLU A 195 CD GLU A 195 OE1 0.085 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 ARG A 224 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 224 NE - CZ - NH2 ANGL. DEV. = -3.0 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 PRO A 69 100.96 -53.53 REMARK 500 ALA A 71 -5.16 56.45 REMARK 500 SER A 76 150.69 -49.42 REMARK 500 LEU A 260 55.73 -141.79 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 A 787 DISTANCE = 6.72 ANGSTROMS REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 405 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 231 OD2 REMARK 620 2 HOH A 754 O 126.8 REMARK 620 N 1 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NAP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MPD A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue EDO A 403 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PGR A 404 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 405 DBREF 6YTZ A -1 349 PDB 6YTZ 6YTZ -1 349 SEQRES 1 A 351 GLY LEU MET ALA ALA SER THR GLU GLY VAL ILE SER ASN SEQRES 2 A 351 LYS GLN VAL ILE LEU LYS ASP TYR VAL THR GLY PHE PRO SEQRES 3 A 351 LYS GLU SER ASP MET GLN LEU THR THR ALA THR THR LYS SEQRES 4 A 351 LEU LYS LEU PRO GLU GLY SER LYS GLY VAL LEU VAL LYS SEQRES 5 A 351 ASN LEU TYR LEU SER CYS ASP PRO TYR MET ARG SER ARG SEQRES 6 A 351 MET THR LYS ARG GLU PRO GLY ALA SER TYR VAL ASP SER SEQRES 7 A 351 PHE ASP ALA GLY SER PRO ILE VAL GLY TYR GLY VAL ALA SEQRES 8 A 351 LYS VAL LEU GLU SER GLY ASP PRO LYS PHE LYS LYS GLY SEQRES 9 A 351 ASP LEU ILE TRP GLY MET THR GLY TRP GLU GLU TYR SER SEQRES 10 A 351 VAL ILE THR SER THR GLU SER LEU PHE LYS ILE GLN HIS SEQRES 11 A 351 ILE ASP VAL PRO LEU SER TYR TYR THR GLY ILE LEU GLY SEQRES 12 A 351 MET PRO GLY MET THR ALA TYR ALA GLY PHE TYR GLU ILE SEQRES 13 A 351 CYS ASN PRO LYS LYS GLY GLU THR VAL PHE VAL SER ALA SEQRES 14 A 351 ALA SER GLY ALA VAL GLY GLN LEU VAL GLY GLN PHE ALA SEQRES 15 A 351 LYS LEU LEU GLY CYS TYR VAL VAL GLY SER ALA GLY SER SEQRES 16 A 351 LYS GLU LYS VAL ASP LEU LEU LYS ASN LYS PHE GLY PHE SEQRES 17 A 351 ASP ASN ALA PHE ASN TYR LYS GLU GLU PRO ASP LEU ASP SEQRES 18 A 351 ALA ALA LEU LYS ARG TYR PHE PRO GLU GLY ILE ASP ILE SEQRES 19 A 351 TYR PHE GLU ASN VAL GLY GLY VAL MET LEU ASP ALA VAL SEQRES 20 A 351 LEU PRO ASN MET ARG VAL HIS GLY ARG ILE ALA VAL CYS SEQRES 21 A 351 GLY LEU ILE SER GLN TYR ASN ILE ALA ALA ALA GLU GLY SEQRES 22 A 351 CYS ARG ASN LEU MET TYR LEU ILE ILE LYS GLN VAL ARG SEQRES 23 A 351 MET GLN GLY PHE LEU VAL PHE SER TYR TYR HIS LEU TYR SEQRES 24 A 351 GLU LYS PHE LEU GLU MET VAL LEU PRO ALA ILE LYS GLU SEQRES 25 A 351 GLY LYS LEU THR TYR VAL GLU ASP VAL VAL GLU GLY LEU SEQRES 26 A 351 GLU SER ALA PRO ALA ALA LEU ILE GLY LEU TYR ALA GLY SEQRES 27 A 351 ARG ASN VAL GLY LYS GLN VAL VAL VAL VAL SER ARG GLU HET NAP A 401 48 HET MPD A 402 8 HET EDO A 403 4 HET PGR A 404 5 HET NA A 405 1 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM EDO 1,2-ETHANEDIOL HETNAM PGR R-1,2-PROPANEDIOL HETNAM NA SODIUM ION HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE HETSYN EDO ETHYLENE GLYCOL FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 MPD C6 H14 O2 FORMUL 4 EDO C2 H6 O2 FORMUL 5 PGR C3 H8 O2 FORMUL 6 NA NA 1+ FORMUL 7 HOH *287(H2 O) HELIX 1 AA1 LYS A 25 SER A 27 5 3 HELIX 2 AA2 ASP A 57 THR A 65 5 9 HELIX 3 AA3 PRO A 132 GLY A 138 5 7 HELIX 4 AA4 GLY A 141 CYS A 155 1 15 HELIX 5 AA5 VAL A 172 GLY A 184 1 13 HELIX 6 AA6 SER A 193 LYS A 203 1 11 HELIX 7 AA7 LYS A 213 GLU A 215 5 3 HELIX 8 AA8 ASP A 217 PHE A 226 1 10 HELIX 9 AA9 GLY A 238 LEU A 246 1 9 HELIX 10 AB1 LEU A 260 TYR A 264 5 5 HELIX 11 AB2 LEU A 275 LYS A 281 1 7 HELIX 12 AB3 LEU A 289 HIS A 295 5 7 HELIX 13 AB4 LEU A 296 GLU A 310 1 15 HELIX 14 AB5 SER A 325 LEU A 333 1 9 HELIX 15 AB6 TYR A 334 GLY A 336 5 3 SHEET 1 AA1 2 ILE A 9 LEU A 16 0 SHEET 2 AA1 2 MET A 29 THR A 36 -1 O THR A 36 N ILE A 9 SHEET 1 AA2 5 TYR A 114 ILE A 117 0 SHEET 2 AA2 5 VAL A 47 SER A 55 -1 N VAL A 47 O ILE A 117 SHEET 3 AA2 5 VAL A 84 SER A 94 -1 O LEU A 92 N LEU A 48 SHEET 4 AA2 5 LEU A 104 GLY A 110 -1 O THR A 109 N GLY A 85 SHEET 5 AA2 5 PHE A 124 LYS A 125 -1 O PHE A 124 N TRP A 106 SHEET 1 AA3 4 TYR A 114 ILE A 117 0 SHEET 2 AA3 4 VAL A 47 SER A 55 -1 N VAL A 47 O ILE A 117 SHEET 3 AA3 4 LYS A 341 VAL A 345 -1 O VAL A 344 N LEU A 54 SHEET 4 AA3 4 GLU A 317 GLU A 321 1 N ASP A 318 O VAL A 343 SHEET 1 AA4 6 ASN A 208 ASN A 211 0 SHEET 2 AA4 6 TYR A 186 ALA A 191 1 N ALA A 191 O PHE A 210 SHEET 3 AA4 6 THR A 162 VAL A 165 1 N VAL A 163 O TYR A 186 SHEET 4 AA4 6 ILE A 230 GLU A 235 1 O PHE A 234 N PHE A 164 SHEET 5 AA4 6 MET A 249 VAL A 257 1 O ARG A 250 N ILE A 230 SHEET 6 AA4 6 ARG A 284 GLY A 287 1 O GLN A 286 N ILE A 255 LINK OD2 ASP A 231 NA NA A 405 1555 1555 2.56 LINK NA NA A 405 O HOH A 754 1555 1555 2.68 SITE 1 AC1 38 PRO A 58 MET A 142 THR A 146 GLY A 170 SITE 2 AC1 38 ALA A 171 VAL A 172 ALA A 191 GLY A 192 SITE 3 AC1 38 LYS A 196 TYR A 212 ASN A 236 VAL A 237 SITE 4 AC1 38 CYS A 258 GLY A 259 LEU A 260 ILE A 261 SITE 5 AC1 38 SER A 262 TYR A 264 PHE A 288 LEU A 289 SITE 6 AC1 38 VAL A 290 LEU A 333 TYR A 334 GLY A 336 SITE 7 AC1 38 ASN A 338 EDO A 403 HOH A 536 HOH A 537 SITE 8 AC1 38 HOH A 587 HOH A 592 HOH A 603 HOH A 621 SITE 9 AC1 38 HOH A 622 HOH A 637 HOH A 638 HOH A 641 SITE 10 AC1 38 HOH A 691 HOH A 782 SITE 1 AC2 4 TRP A 106 SER A 122 TYR A 294 TYR A 297 SITE 1 AC3 6 TYR A 212 LYS A 213 TYR A 334 ALA A 335 SITE 2 AC3 6 GLY A 336 NAP A 401 SITE 1 AC4 3 TYR A 59 TYR A 73 HOH A 523 SITE 1 AC5 4 GLY A 160 ASP A 231 ARG A 250 HOH A 754 CRYST1 68.545 68.645 145.398 90.00 90.00 90.00 I 2 2 2 8 ORIGX1 1.000000 0.000000 0.000000 0.00000 ORIGX2 0.000000 1.000000 0.000000 0.00000 ORIGX3 0.000000 0.000000 1.000000 0.00000 SCALE1 0.014589 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014568 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006878 0.00000