HEADER BIOSYNTHETIC PROTEIN 21-APR-20 6YSB TITLE CRYSTAL STRUCTURE OF MALUS DOMESTICA DOUBLE BOND REDUCTASE (MDDBR) APO TITLE 2 FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-ALKENAL REDUCTASE (NADP(+)-DEPENDENT)-LIKE; COMPND 3 CHAIN: B, A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYRUS USSURIENSIS X PYRUS COMMUNIS; SOURCE 3 ORGANISM_TAXID: 2448454; SOURCE 4 GENE: D8674_014777; 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 6YSB 1 REMARK REVDAT 1 03-FEB-21 6YSB 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. 1.20 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 : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.62 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 3 NUMBER OF REFLECTIONS : 200156 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) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.198 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 10528 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) : 1.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 14893 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.84 REMARK 3 BIN R VALUE (WORKING SET) : 0.2390 REMARK 3 BIN FREE R VALUE SET COUNT : 734 REMARK 3 BIN FREE R VALUE : 0.2850 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5261 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 527 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 24.00 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.36000 REMARK 3 B22 (A**2) : -0.91000 REMARK 3 B33 (A**2) : -0.02000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.72000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.039 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.041 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.045 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.381 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.974 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.965 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5379 ; 0.018 ; 0.013 REMARK 3 BOND LENGTHS OTHERS (A): 5123 ; 0.004 ; 0.017 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7257 ; 2.126 ; 1.640 REMARK 3 BOND ANGLES OTHERS (DEGREES): 11906 ; 1.601 ; 1.577 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 674 ; 7.018 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 236 ;36.243 ;23.220 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 955 ;13.702 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;16.291 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 670 ; 0.123 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5938 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 1091 ; 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): 10497 ;11.434 ; 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 : NULL 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 6YSB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-APR-20. REMARK 100 THE DEPOSITION ID IS D_1292108045. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 04-JUN-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) : 1.0 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 : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 210636 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 48.720 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 3.600 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) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.22 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: 2J3H REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.14 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 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, TEMPERATURE 293.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 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+1/2,Y+1/2,Z REMARK 290 4555 -X+1/2,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 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 78.30450 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.33300 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 78.30450 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 34.33300 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 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 B 1 REMARK 465 ALA B 2 REMARK 465 ALA B 3 REMARK 465 SER B 4 REMARK 465 THR B 5 REMARK 465 GLU B 6 REMARK 465 GLY B 7 REMARK 465 VAL B 8 REMARK 465 TYR B 73 REMARK 465 VAL B 74 REMARK 465 MET A 1 REMARK 465 ALA A 2 REMARK 465 ALA A 3 REMARK 465 SER A 4 REMARK 465 THR A 5 REMARK 465 GLU A 6 REMARK 465 GLY A 7 REMARK 465 VAL A 8 REMARK 465 TYR A 73 REMARK 465 VAL A 74 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LYS B 45 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 CD1 ILE A 154 O HOH A 744 0.54 REMARK 500 CG LYS A 208 O HOH A 753 1.27 REMARK 500 O HOH A 673 O HOH A 729 1.27 REMARK 500 C ASN B 202 O HOH B 502 1.35 REMARK 500 O HOH A 703 O HOH A 740 1.35 REMARK 500 O HOH A 554 O HOH A 681 1.42 REMARK 500 O HOH B 641 O HOH B 678 1.43 REMARK 500 CD1 PHE A 300 O HOH A 727 1.47 REMARK 500 O HOH A 782 O HOH A 785 1.47 REMARK 500 OE1 GLU A 317 O HOH A 501 1.47 REMARK 500 O HOH A 693 O HOH A 782 1.48 REMARK 500 O ILE B 331 O HOH B 501 1.48 REMARK 500 OH TYR A 315 O HOH A 502 1.48 REMARK 500 O ASN B 202 O HOH B 502 1.51 REMARK 500 O HOH A 584 O HOH A 715 1.52 REMARK 500 OH TYR B 315 O HOH B 503 1.53 REMARK 500 O HOH B 651 O HOH B 710 1.54 REMARK 500 O HOH A 749 O HOH A 775 1.55 REMARK 500 O HOH B 701 O HOH B 710 1.57 REMARK 500 O HOH A 787 O HOH A 805 1.58 REMARK 500 CG1 ILE A 154 O HOH A 744 1.58 REMARK 500 O HOH A 782 O HOH A 802 1.61 REMARK 500 O HOH B 701 O HOH B 709 1.61 REMARK 500 O TYR B 334 O HOH B 504 1.63 REMARK 500 O HOH A 762 O HOH A 802 1.66 REMARK 500 O HOH A 740 O HOH A 775 1.66 REMARK 500 O HOH A 659 O HOH A 740 1.67 REMARK 500 O HOH B 689 O HOH B 710 1.67 REMARK 500 O HOH B 692 O HOH B 699 1.68 REMARK 500 CB ALA A 171 O HOH A 507 1.69 REMARK 500 O HOH B 503 O HOH B 535 1.71 REMARK 500 O HOH A 501 O HOH A 539 1.74 REMARK 500 O HOH B 574 O HOH B 638 1.75 REMARK 500 O HOH A 801 O HOH A 807 1.76 REMARK 500 CB GLU A 93 O HOH A 542 1.78 REMARK 500 CB ALA A 171 O HOH A 731 1.80 REMARK 500 O HOH A 521 O HOH A 562 1.80 REMARK 500 CG1 ILE B 105 O HOH B 680 1.85 REMARK 500 O HOH A 518 O HOH A 531 1.86 REMARK 500 O HOH B 544 O HOH B 588 1.86 REMARK 500 C VAL B 343 O HOH B 505 1.90 REMARK 500 O HOH B 615 O HOH B 678 1.92 REMARK 500 O HOH A 502 O HOH A 539 1.92 REMARK 500 O HOH B 615 O HOH B 699 1.93 REMARK 500 CE1 PHE A 300 O HOH A 727 1.93 REMARK 500 O VAL B 343 O HOH B 505 1.94 REMARK 500 O HOH B 689 O HOH B 702 1.96 REMARK 500 N LYS B 203 O HOH B 502 1.96 REMARK 500 O HOH A 608 O HOH A 681 1.97 REMARK 500 CB TYR B 334 O HOH B 501 1.99 REMARK 500 REMARK 500 THIS ENTRY HAS 69 CLOSE CONTACTS 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 696 O HOH A 801 4446 1.75 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 B 195 CD GLU B 195 OE2 -0.067 REMARK 500 GLU B 268 CD GLU B 268 OE1 0.072 REMARK 500 ARG A 61 C ARG A 61 O 0.115 REMARK 500 ARG A 63 C MET A 64 N 0.237 REMARK 500 SER A 72 CB SER A 72 OG 0.083 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 B 334 CB - CG - CD1 ANGL. DEV. = 4.0 DEGREES REMARK 500 ALA A 171 N - CA - CB ANGL. DEV. = 9.3 DEGREES REMARK 500 GLU A 235 OE1 - CD - OE2 ANGL. DEV. = 7.9 DEGREES REMARK 500 MET A 303 CG - SD - CE ANGL. DEV. = -13.6 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 GLU B 68 -149.98 -81.65 REMARK 500 PRO B 69 48.88 -82.91 REMARK 500 ASP B 130 35.52 -78.84 REMARK 500 ARG A 61 -57.13 -26.90 REMARK 500 ARG A 63 -8.73 -55.51 REMARK 500 PRO A 69 107.86 -41.84 REMARK 500 ALA A 71 -169.57 -109.30 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 GLN A 263 -10.42 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 B 718 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH B 719 DISTANCE = 6.04 ANGSTROMS REMARK 525 HOH A 808 DISTANCE = 6.06 ANGSTROMS REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 B 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SO4 A 401 DBREF 6YSB B 1 349 PDB 6YSB 6YSB 1 349 DBREF 6YSB A 1 349 PDB 6YSB 6YSB 1 349 SEQRES 1 B 349 MET ALA ALA SER THR GLU GLY VAL ILE SER ASN LYS GLN SEQRES 2 B 349 VAL ILE LEU LYS ASP TYR VAL THR GLY PHE PRO LYS GLU SEQRES 3 B 349 SER ASP MET GLN LEU THR THR ALA THR THR LYS LEU LYS SEQRES 4 B 349 LEU PRO GLU GLY SER LYS GLY VAL LEU VAL LYS ASN LEU SEQRES 5 B 349 TYR LEU SER CYS ASP PRO TYR MET ARG SER ARG MET THR SEQRES 6 B 349 LYS ARG GLU PRO GLY ALA SER TYR VAL ASP SER PHE ASP SEQRES 7 B 349 ALA GLY SER PRO ILE VAL GLY TYR GLY VAL ALA LYS VAL SEQRES 8 B 349 LEU GLU SER GLY ASP PRO LYS PHE LYS LYS GLY ASP LEU SEQRES 9 B 349 ILE TRP GLY MET THR GLY TRP GLU GLU TYR SER VAL ILE SEQRES 10 B 349 THR SER THR GLU SER LEU PHE LYS ILE GLN HIS ILE ASP SEQRES 11 B 349 VAL PRO LEU SER TYR TYR THR GLY ILE LEU GLY MET PRO SEQRES 12 B 349 GLY MET THR ALA TYR ALA GLY PHE TYR GLU ILE CYS ASN SEQRES 13 B 349 PRO LYS LYS GLY GLU THR VAL PHE VAL SER ALA ALA SER SEQRES 14 B 349 GLY ALA VAL GLY GLN LEU VAL GLY GLN PHE ALA LYS LEU SEQRES 15 B 349 LEU GLY CYS TYR VAL VAL GLY SER ALA GLY SER LYS GLU SEQRES 16 B 349 LYS VAL ASP LEU LEU LYS ASN LYS PHE GLY PHE ASP LYS SEQRES 17 B 349 ALA PHE ASN TYR LYS GLU GLU PRO ASP LEU ASP ALA ALA SEQRES 18 B 349 LEU LYS ARG TYR PHE PRO GLU GLY ILE ASP ILE TYR PHE SEQRES 19 B 349 GLU ASN VAL GLY GLY LYS MET LEU ASP ALA VAL LEU PRO SEQRES 20 B 349 ASN MET ARG VAL HIS GLY ARG ILE ALA VAL CYS GLY LEU SEQRES 21 B 349 ILE SER GLN TYR ASN ILE ASP GLU PRO GLU GLY CYS ARG SEQRES 22 B 349 ASN LEU MET TYR LEU ILE ILE LYS GLN VAL ARG MET GLN SEQRES 23 B 349 GLY PHE LEU VAL PHE SER TYR TYR HIS LEU TYR GLU LYS SEQRES 24 B 349 PHE LEU GLU MET VAL LEU PRO ALA ILE LYS GLU GLY LYS SEQRES 25 B 349 LEU THR TYR VAL GLU ASP VAL VAL GLU GLY LEU GLU SER SEQRES 26 B 349 ALA PRO ALA ALA LEU ILE GLY LEU TYR ALA GLY ARG ASN SEQRES 27 B 349 VAL GLY LYS GLN VAL VAL VAL VAL SER ARG GLU SEQRES 1 A 349 MET ALA ALA SER THR GLU GLY VAL ILE SER ASN LYS GLN SEQRES 2 A 349 VAL ILE LEU LYS ASP TYR VAL THR GLY PHE PRO LYS GLU SEQRES 3 A 349 SER ASP MET GLN LEU THR THR ALA THR THR LYS LEU LYS SEQRES 4 A 349 LEU PRO GLU GLY SER LYS GLY VAL LEU VAL LYS ASN LEU SEQRES 5 A 349 TYR LEU SER CYS ASP PRO TYR MET ARG SER ARG MET THR SEQRES 6 A 349 LYS ARG GLU PRO GLY ALA SER TYR VAL ASP SER PHE ASP SEQRES 7 A 349 ALA GLY SER PRO ILE VAL GLY TYR GLY VAL ALA LYS VAL SEQRES 8 A 349 LEU GLU SER GLY ASP PRO LYS PHE LYS LYS GLY ASP LEU SEQRES 9 A 349 ILE TRP GLY MET THR GLY TRP GLU GLU TYR SER VAL ILE SEQRES 10 A 349 THR SER THR GLU SER LEU PHE LYS ILE GLN HIS ILE ASP SEQRES 11 A 349 VAL PRO LEU SER TYR TYR THR GLY ILE LEU GLY MET PRO SEQRES 12 A 349 GLY MET THR ALA TYR ALA GLY PHE TYR GLU ILE CYS ASN SEQRES 13 A 349 PRO LYS LYS GLY GLU THR VAL PHE VAL SER ALA ALA SER SEQRES 14 A 349 GLY ALA VAL GLY GLN LEU VAL GLY GLN PHE ALA LYS LEU SEQRES 15 A 349 LEU GLY CYS TYR VAL VAL GLY SER ALA GLY SER LYS GLU SEQRES 16 A 349 LYS VAL ASP LEU LEU LYS ASN LYS PHE GLY PHE ASP LYS SEQRES 17 A 349 ALA PHE ASN TYR LYS GLU GLU PRO ASP LEU ASP ALA ALA SEQRES 18 A 349 LEU LYS ARG TYR PHE PRO GLU GLY ILE ASP ILE TYR PHE SEQRES 19 A 349 GLU ASN VAL GLY GLY LYS MET LEU ASP ALA VAL LEU PRO SEQRES 20 A 349 ASN MET ARG VAL HIS GLY ARG ILE ALA VAL CYS GLY LEU SEQRES 21 A 349 ILE SER GLN TYR ASN ILE ASP GLU PRO GLU GLY CYS ARG SEQRES 22 A 349 ASN LEU MET TYR LEU ILE ILE LYS GLN VAL ARG MET GLN SEQRES 23 A 349 GLY PHE LEU VAL PHE SER TYR TYR HIS LEU TYR GLU LYS SEQRES 24 A 349 PHE LEU GLU MET VAL LEU PRO ALA ILE LYS GLU GLY LYS SEQRES 25 A 349 LEU THR TYR VAL GLU ASP VAL VAL GLU GLY LEU GLU SER SEQRES 26 A 349 ALA PRO ALA ALA LEU ILE GLY LEU TYR ALA GLY ARG ASN SEQRES 27 A 349 VAL GLY LYS GLN VAL VAL VAL VAL SER ARG GLU HET SO4 B 401 5 HET SO4 A 401 5 HETNAM SO4 SULFATE ION FORMUL 3 SO4 2(O4 S 2-) FORMUL 5 HOH *527(H2 O) HELIX 1 AA1 LYS B 25 SER B 27 5 3 HELIX 2 AA2 ASP B 57 THR B 65 5 9 HELIX 3 AA3 PRO B 132 GLY B 138 5 7 HELIX 4 AA4 GLY B 141 CYS B 155 1 15 HELIX 5 AA5 GLY B 170 GLY B 184 1 15 HELIX 6 AA6 SER B 193 LYS B 203 1 11 HELIX 7 AA7 LYS B 213 GLU B 215 5 3 HELIX 8 AA8 ASP B 217 PHE B 226 1 10 HELIX 9 AA9 GLY B 238 LEU B 246 1 9 HELIX 10 AB1 LEU B 260 ASN B 265 5 6 HELIX 11 AB2 LEU B 275 LYS B 281 1 7 HELIX 12 AB3 LEU B 289 HIS B 295 5 7 HELIX 13 AB4 LEU B 296 GLU B 310 1 15 HELIX 14 AB5 SER B 325 ALA B 335 1 11 HELIX 15 AB6 LYS A 25 SER A 27 5 3 HELIX 16 AB7 PRO A 58 MET A 64 1 7 HELIX 17 AB8 PRO A 132 GLY A 138 5 7 HELIX 18 AB9 GLY A 141 CYS A 155 1 15 HELIX 19 AC1 GLY A 170 GLY A 184 1 15 HELIX 20 AC2 SER A 193 LYS A 203 1 11 HELIX 21 AC3 LYS A 213 GLU A 215 5 3 HELIX 22 AC4 ASP A 217 PHE A 226 1 10 HELIX 23 AC5 GLY A 238 LEU A 246 1 9 HELIX 24 AC6 LEU A 260 ASN A 265 5 6 HELIX 25 AC7 LEU A 275 LYS A 281 1 7 HELIX 26 AC8 LEU A 289 HIS A 295 5 7 HELIX 27 AC9 LEU A 296 GLU A 310 1 15 HELIX 28 AD1 SER A 325 ALA A 335 1 11 SHEET 1 AA1 2 SER B 10 LEU B 16 0 SHEET 2 AA1 2 MET B 29 THR B 35 -1 O ALA B 34 N ASN B 11 SHEET 1 AA2 5 TYR B 114 ILE B 117 0 SHEET 2 AA2 5 VAL B 47 CYS B 56 -1 N VAL B 47 O ILE B 117 SHEET 3 AA2 5 VAL B 84 SER B 94 -1 O LEU B 92 N LEU B 48 SHEET 4 AA2 5 LEU B 104 GLY B 110 -1 O ILE B 105 N ALA B 89 SHEET 5 AA2 5 LEU B 123 LYS B 125 -1 O PHE B 124 N TRP B 106 SHEET 1 AA3 4 TYR B 114 ILE B 117 0 SHEET 2 AA3 4 VAL B 47 CYS B 56 -1 N VAL B 47 O ILE B 117 SHEET 3 AA3 4 LYS B 341 VAL B 345 -1 O VAL B 344 N LEU B 54 SHEET 4 AA3 4 GLU B 317 GLU B 321 1 N VAL B 320 O VAL B 345 SHEET 1 AA4 6 LYS B 208 ASN B 211 0 SHEET 2 AA4 6 TYR B 186 ALA B 191 1 N ALA B 191 O PHE B 210 SHEET 3 AA4 6 THR B 162 VAL B 165 1 N VAL B 163 O TYR B 186 SHEET 4 AA4 6 ILE B 230 GLU B 235 1 O PHE B 234 N PHE B 164 SHEET 5 AA4 6 MET B 249 VAL B 257 1 O ARG B 250 N ILE B 230 SHEET 6 AA4 6 ARG B 284 GLY B 287 1 O GLN B 286 N ILE B 255 SHEET 1 AA5 2 SER A 10 LEU A 16 0 SHEET 2 AA5 2 MET A 29 THR A 35 -1 O GLN A 30 N ILE A 15 SHEET 1 AA6 5 TYR A 114 ILE A 117 0 SHEET 2 AA6 5 VAL A 47 CYS A 56 -1 N VAL A 47 O ILE A 117 SHEET 3 AA6 5 VAL A 84 SER A 94 -1 O LEU A 92 N LEU A 48 SHEET 4 AA6 5 LEU A 104 GLY A 110 -1 O ILE A 105 N ALA A 89 SHEET 5 AA6 5 PHE A 124 LYS A 125 -1 O PHE A 124 N TRP A 106 SHEET 1 AA7 4 TYR A 114 ILE A 117 0 SHEET 2 AA7 4 VAL A 47 CYS A 56 -1 N VAL A 47 O ILE A 117 SHEET 3 AA7 4 LYS A 341 VAL A 345 -1 O VAL A 344 N LEU A 54 SHEET 4 AA7 4 GLU A 317 GLU A 321 1 N ASP A 318 O LYS A 341 SHEET 1 AA8 6 LYS A 208 ASN A 211 0 SHEET 2 AA8 6 TYR A 186 ALA A 191 1 N ALA A 191 O PHE A 210 SHEET 3 AA8 6 THR A 162 VAL A 165 1 N VAL A 163 O TYR A 186 SHEET 4 AA8 6 ILE A 230 GLU A 235 1 O ILE A 232 N PHE A 164 SHEET 5 AA8 6 MET A 249 VAL A 257 1 O ARG A 250 N ILE A 230 SHEET 6 AA8 6 ARG A 284 GLY A 287 1 O ARG A 284 N ILE A 255 SITE 1 AC1 9 ALA B 191 GLY B 192 LYS B 196 TYR B 212 SITE 2 AC1 9 HOH B 541 HOH B 546 HOH B 623 HOH B 629 SITE 3 AC1 9 HOH B 630 SITE 1 AC2 10 ALA A 191 GLY A 192 LYS A 196 TYR A 212 SITE 2 AC2 10 HOH A 518 HOH A 525 HOH A 531 HOH A 552 SITE 3 AC2 10 HOH A 555 HOH A 584 CRYST1 156.609 68.666 68.944 90.00 111.38 90.00 C 1 2 1 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 0.006385 0.000000 0.002499 0.00000 SCALE2 0.000000 0.014563 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015576 0.00000