HEADER BIOSYNTHETIC PROTEIN 27-APR-20 6YUX TITLE CRYSTAL STRUCTURE OF MALUS DOMESTICA DOUBLE BOND REDUCTASE (MDDBR) TITLE 2 TERNARY COMPLEX 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 6YUX 1 REMARK REVDAT 1 03-FEB-21 6YUX 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. 1.36 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0238 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) : 1.36 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.52 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 3 NUMBER OF REFLECTIONS : 69315 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) : 0.145 REMARK 3 R VALUE (WORKING SET) : 0.143 REMARK 3 FREE R VALUE : 0.179 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 3570 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) : 1.37 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.40 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4728 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 92.69 REMARK 3 BIN R VALUE (WORKING SET) : 0.5200 REMARK 3 BIN FREE R VALUE SET COUNT : 239 REMARK 3 BIN FREE R VALUE : 0.5750 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2640 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 76 REMARK 3 SOLVENT ATOMS : 197 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : 0.02000 REMARK 3 B33 (A**2) : -0.03000 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): 0.052 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.051 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.035 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.050 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.970 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2769 ; 0.017 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 2615 ; 0.001 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3744 ; 2.011 ; 1.675 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6064 ; 1.566 ; 1.591 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 339 ; 7.136 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 116 ;37.972 ;23.362 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 473 ;13.851 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;17.043 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 348 ; 0.126 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3029 ; 0.014 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 567 ; 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): 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): 5383 ; 4.051 ; 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 6YUX COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 27-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292108314. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAR-19 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 : 11.2C 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 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 72885 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.360 REMARK 200 RESOLUTION RANGE LOW (A) : 48.520 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.36 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.39 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 (%): 44.85 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.23 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 12.5% (W/V) PEG 1000, 12.5% (W/V) PEG REMARK 280 3350, 12.5% (W/V) MPD, 0.03 M MAGNESIUM CHLORIDE, 0.03 M CALCIUM REMARK 280 CHLORIDE, 0.03 M SODIUM CHLORIDE, 0.03 M SODIUM BROMIDE, 0.03 M REMARK 280 SODIUM IODIDE IN 0.1 M MES/IMIDAZOLE PH 6.5, VAPOR DIFFUSION, REMARK 280 HANGING DROP, 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 34.24550 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 34.30550 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 72.98450 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 34.24550 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 34.30550 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 72.98450 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 34.24550 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 34.30550 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 72.98450 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 34.24550 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 34.30550 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 72.98450 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2730 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 14710 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -32.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 562 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 688 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 694 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 GLU A 68 REMARK 465 PRO A 69 REMARK 465 GLY A 70 REMARK 465 ALA A 71 REMARK 465 SER A 72 REMARK 465 TYR A 73 REMARK 465 GLU A 268 REMARK 465 PRO A 269 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 619 O HOH A 664 1.68 REMARK 500 O HOH A 683 O HOH A 684 2.11 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 42 CD GLU A 42 OE1 -0.094 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 TYR A 135 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 224 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 ARG A 224 NE - CZ - NH2 ANGL. DEV. = -3.1 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 ASP A 130 30.62 -91.29 REMARK 500 ILE A 266 147.81 -175.27 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 696 DISTANCE = 5.98 ANGSTROMS REMARK 525 HOH A 697 DISTANCE = 6.77 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 677 O 102.8 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 406 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ILE A 261 O REMARK 620 2 HOH A 611 O 93.4 REMARK 620 3 HOH A 693 O 117.8 113.1 REMARK 620 N 1 2 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 FER 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 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 406 DBREF 6YUX A 0 349 PDB 6YUX 6YUX 0 349 SEQRES 1 A 350 MET ALA ALA ALA SER THR GLU GLY VAL ILE SER ASN LYS SEQRES 2 A 350 GLN VAL ILE LEU LYS ASP TYR VAL THR GLY PHE PRO LYS SEQRES 3 A 350 GLU SER ASP MET GLN LEU THR THR ALA THR THR LYS LEU SEQRES 4 A 350 LYS LEU PRO GLU GLY SER LYS GLY VAL LEU VAL LYS ASN SEQRES 5 A 350 LEU TYR LEU SER CYS ASP PRO TYR MET ARG SER ARG MET SEQRES 6 A 350 THR LYS ARG GLU PRO GLY ALA SER TYR ALA ALA SER PHE SEQRES 7 A 350 ASP ALA GLY SER PRO ILE VAL GLY TYR GLY VAL ALA LYS SEQRES 8 A 350 VAL LEU GLU SER GLY ASP PRO LYS PHE LYS LYS GLY ASP SEQRES 9 A 350 LEU ILE TRP GLY MET THR GLY TRP GLU GLU TYR SER VAL SEQRES 10 A 350 ILE THR SER THR GLU SER LEU PHE LYS ILE GLN HIS ILE SEQRES 11 A 350 ASP VAL PRO LEU SER TYR TYR THR GLY ILE LEU GLY MET SEQRES 12 A 350 PRO GLY MET THR ALA TYR ALA GLY PHE TYR GLU ILE CYS SEQRES 13 A 350 ASN PRO LYS LYS GLY GLU THR VAL PHE VAL SER ALA ALA SEQRES 14 A 350 SER GLY ALA VAL GLY GLN LEU VAL GLY GLN PHE ALA LYS SEQRES 15 A 350 LEU LEU GLY CYS TYR VAL VAL GLY SER ALA GLY SER LYS SEQRES 16 A 350 GLU LYS VAL ASP LEU LEU LYS ASN LYS PHE GLY PHE ASP SEQRES 17 A 350 ASN ALA PHE ASN TYR LYS GLU GLU PRO ASP LEU ASP ALA SEQRES 18 A 350 ALA LEU LYS ARG TYR PHE PRO GLU GLY ILE ASP ILE TYR SEQRES 19 A 350 PHE GLU ASN VAL GLY GLY VAL MET LEU ASP ALA VAL LEU SEQRES 20 A 350 PRO ASN MET ARG VAL HIS GLY ARG ILE ALA VAL CYS GLY SEQRES 21 A 350 LEU ILE SER GLN TYR ASN ILE ASP GLU PRO GLU GLY CYS SEQRES 22 A 350 HIS ASN LEU MET TYR LEU ILE ILE LYS GLN VAL ARG MET SEQRES 23 A 350 GLN GLY PHE LEU VAL PHE SER TYR TYR HIS LEU TYR GLU SEQRES 24 A 350 LYS PHE LEU GLU MET VAL LEU PRO ALA ILE LYS GLU GLY SEQRES 25 A 350 LYS LEU THR TYR VAL GLU ASP VAL VAL GLU GLY LEU GLU SEQRES 26 A 350 SER ALA PRO ALA ALA LEU ILE GLY LEU TYR ALA GLY ARG SEQRES 27 A 350 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 FER A 404 14 HET NA A 405 1 HET NA A 406 1 HETNAM NAP NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE HETNAM MPD (4S)-2-METHYL-2,4-PENTANEDIOL HETNAM EDO 1,2-ETHANEDIOL HETNAM FER 3-(4-HYDROXY-3-METHOXYPHENYL)-2-PROPENOIC ACID HETNAM NA SODIUM ION HETSYN NAP 2'-MONOPHOSPHOADENOSINE 5'-DIPHOSPHORIBOSE HETSYN EDO ETHYLENE GLYCOL HETSYN FER FERULIC ACID FORMUL 2 NAP C21 H28 N7 O17 P3 FORMUL 3 MPD C6 H14 O2 FORMUL 4 EDO C2 H6 O2 FORMUL 5 FER C10 H10 O4 FORMUL 6 NA 2(NA 1+) FORMUL 8 HOH *197(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 VAL A 8 LEU A 16 0 SHEET 2 AA1 2 MET A 29 LYS A 37 -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 ARG A 284 N ILE A 255 LINK OD2 ASP A 231 NA NA A 405 1555 1555 2.76 LINK O ILE A 261 NA NA A 406 1555 1555 2.84 LINK NA NA A 405 O HOH A 677 1555 1555 2.11 LINK NA NA A 406 O HOH A 611 1555 1555 2.71 LINK NA NA A 406 O HOH A 693 1555 4545 2.75 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 FER A 404 HOH A 533 SITE 8 AC1 38 HOH A 564 HOH A 565 HOH A 575 HOH A 579 SITE 9 AC1 38 HOH A 580 HOH A 599 HOH A 600 HOH A 633 SITE 10 AC1 38 HOH A 657 HOH A 693 SITE 1 AC2 5 TYR A 86 TRP A 106 SER A 122 TYR A 294 SITE 2 AC2 5 TYR A 297 SITE 1 AC3 7 TYR A 212 LYS A 213 TYR A 334 ALA A 335 SITE 2 AC3 7 GLY A 336 NAP A 401 HOH A 523 SITE 1 AC4 6 TYR A 59 ALA A 74 LEU A 289 PHE A 291 SITE 2 AC4 6 NAP A 401 HOH A 531 SITE 1 AC5 4 GLY A 160 ASP A 231 ARG A 250 HOH A 677 SITE 1 AC6 4 ILE A 261 ASN A 265 HOH A 611 HOH A 693 CRYST1 68.491 68.611 145.969 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 0.014600 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014575 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006851 0.00000