HEADER LYASE 15-MAY-15 5A29 TITLE FAMILY 2 PECTATE LYASE FROM VIBRIO VULNIFICUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: EXOPOLYGALACTURONATE LYASE; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 19-566; COMPND 5 SYNONYM: PECTATE LYASE; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: PECTATE LYASE; COMPND 8 CHAIN: B; COMPND 9 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: VIBRIO VULNIFICUS; SOURCE 3 ORGANISM_TAXID: 196600; SOURCE 4 STRAIN: YJ016; SOURCE 5 MOL_ID: 2; SOURCE 6 SYNTHETIC: YES; SOURCE 7 ORGANISM_SCIENTIFIC: VIBRIO VULNIFICUS; SOURCE 8 ORGANISM_TAXID: 196600; SOURCE 9 OTHER_DETAILS: CUSTOM SYNTHESIZED, CODON OPTIMIZED CODING SEQUENCE KEYWDS LYASE, PECTIN, POLYSACCHARIDE LYASE, ENDOLYTIC, EXOLYTIC, BETA- KEYWDS 2 ELIMINATION, ANCESTRAL GENE RESURRECTION, MAGNESIUM EXPDTA X-RAY DIFFRACTION AUTHOR R.MCLEAN,J.K.HOBBS,M.D.SUITS,S.TUOMIVAARA,D.JONES,A.B.BORASTON, AUTHOR 2 D.W.ABBOTT REVDAT 6 10-JAN-24 5A29 1 REMARK LINK REVDAT 5 15-MAY-19 5A29 1 REMARK REVDAT 4 08-MAY-19 5A29 1 REMARK REVDAT 3 16-SEP-15 5A29 1 JRNL REVDAT 2 22-JUL-15 5A29 1 JRNL REVDAT 1 01-JUL-15 5A29 0 JRNL AUTH R.MCLEAN,J.K.HOBBS,M.D.SUITS,S.T.TUOMIVAARA,D.JONES, JRNL AUTH 2 A.B.BORASTON,D.W.ABBOTT JRNL TITL FUNCTIONAL ANALYSES OF RESURRECTED AND CONTEMPORARY ENZYMES JRNL TITL 2 ILLUMINATE AN EVOLUTIONARY PATH FOR THE EMERGENCE OF JRNL TITL 3 EXOLYSIS IN POLYSACCHARIDE LYASE FAMILY 2. JRNL REF J.BIOL.CHEM. V. 290 21231 2015 JRNL REFN ISSN 0021-9258 JRNL PMID 26160170 JRNL DOI 10.1074/JBC.M115.664847 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0073 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 122.20 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 61132 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) : 0.158 REMARK 3 R VALUE (WORKING SET) : 0.156 REMARK 3 FREE R VALUE : 0.197 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3266 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) : 1.90 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.95 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4409 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.43 REMARK 3 BIN R VALUE (WORKING SET) : 0.2030 REMARK 3 BIN FREE R VALUE SET COUNT : 225 REMARK 3 BIN FREE R VALUE : 0.2570 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4526 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 79 REMARK 3 SOLVENT ATOMS : 498 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.83 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.58000 REMARK 3 B22 (A**2) : -0.58000 REMARK 3 B33 (A**2) : 1.90000 REMARK 3 B12 (A**2) : -0.29000 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): 0.107 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.111 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.072 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.439 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.970 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.951 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4755 ; 0.020 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6447 ; 1.907 ; 1.950 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 576 ; 6.696 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 239 ;37.292 ;23.933 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 750 ;13.360 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 30 ;16.993 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 680 ; 0.164 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3706 ; 0.013 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 2274 ; 2.970 ; 2.442 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2842 ; 3.681 ; 3.630 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2481 ; 4.261 ; 2.808 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): 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. U VALUES REFINED INDIVIDUALLY. RESIDUES 0-17 THAT REMARK 3 INCLUDE THE HISTIDINE-AFFINITY TAG, INTERDIGITATE FROM AN REMARK 3 ADJACENT PROTEIN MOLECULE REMARK 4 REMARK 4 5A29 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 15-MAY-15. REMARK 100 THE DEPOSITION ID IS D_1290063796. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL12-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : LIQUID NITROGEN-COOLED DOUBLE REMARK 200 CRYSTAL SI(111) REMARK 200 OPTICS : MIRRORS RH COATED REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 64624 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 122.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.800 REMARK 200 R MERGE (I) : 0.10000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 29.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 5.00 REMARK 200 R MERGE FOR SHELL (I) : 0.42000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.600 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 2V8J REMARK 200 REMARK 200 REMARK: NONE REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.60 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.20 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: CRYSTALS OF VVPL2 DEVELOPED VIA REMARK 280 HANGING DROP VAPOUR DIFFUSION METHOD AT A PROTEIN CONCENTRATION REMARK 280 OF 15 MG/ML BY MIXING EQUAL AMOUNTS OF THE PROTEIN SOLUTION WITH REMARK 280 A MOTHER LIQUOR CONSISTING OF 16% (W/V) POLYETHYLENE GLYCOL 3, REMARK 280 350, 0.14 M NA/K TARTRATE, AND 0.1 M HEPES (PH 7.0) AT 19 REMARK 280 DEGREES CELSIUS. CRYSTALS WERE CRYOPROTECTED BY BRIEF CRYSTAL REMARK 280 IMMERSION INTO A SOLUTION OF THE RESERVOIR SOLUTION SUPPLEMENTED REMARK 280 WITH 25% ETHYLENE GLYCOL, AND SUBSEQUENTLY FROZEN IN A LIQUID REMARK 280 NITROGEN STREAM PRIOR TO DIFFRACTION EXPERIMENTS., VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 65 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/6 REMARK 290 6555 X-Y,X,Z+5/6 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.28400 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 24.14200 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 36.21300 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 12.07100 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 60.35500 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: 5530 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 21260 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 24.1 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 -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 SER A 0 REMARK 465 HIS A 1 REMARK 465 HIS A 2 REMARK 465 HIS A 3 REMARK 465 HIS A 4 REMARK 465 HIS A 5 REMARK 465 HIS A 6 REMARK 465 SER A 7 REMARK 465 SER A 8 REMARK 465 GLY A 9 REMARK 465 LEU A 10 REMARK 465 VAL A 11 REMARK 465 PRO A 12 REMARK 465 ARG A 13 REMARK 465 GLY A 14 REMARK 465 SER A 15 REMARK 465 HIS A 16 REMARK 465 ALA A 17 REMARK 465 MET A 18 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 A 406 CG CD CE NZ REMARK 470 LYS A 408 CG CD CE NZ REMARK 470 HIS B 0 CG ND1 CD2 CE1 NE2 REMARK 470 HIS B 1 CG ND1 CD2 CE1 NE2 REMARK 470 HIS B 3 CG ND1 CD2 CE1 NE2 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 2451 O HOH A 2454 1.68 REMARK 500 O HOH A 2406 O HOH A 2407 2.03 REMARK 500 O HOH A 2415 O HOH A 2430 2.03 REMARK 500 NE2 HIS A 405 O HOH A 2316 2.12 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 N ALA A 19 C ALA B 17 4784 2.12 REMARK 500 CB LYS A 406 O HOH A 2102 4785 2.12 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 507 NE - CZ - NH2 ANGL. DEV. = -3.6 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 ASN A 146 53.71 -141.57 REMARK 500 ASP A 165 85.74 -152.23 REMARK 500 THR A 224 -142.67 -139.95 REMARK 500 LEU A 227 59.78 -92.55 REMARK 500 SER A 326 -1.56 66.86 REMARK 500 PHE A 333 -73.17 -115.32 REMARK 500 GLU A 410 36.33 -78.90 REMARK 500 ALA A 424 67.46 -68.25 REMARK 500 SER A 540 17.48 80.81 REMARK 500 ALA A 550 -123.11 49.13 REMARK 500 ILE A 561 -60.22 -105.80 REMARK 500 REMARK 500 REMARK: NULL 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 MN A 601 MN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 129 NE2 REMARK 620 2 GLU A 150 OE1 85.6 REMARK 620 3 HIS A 192 NE2 93.5 84.2 REMARK 620 4 HOH A2137 O 88.2 93.6 177.1 REMARK 620 5 HIS B 4 NE2 99.8 172.5 100.6 81.4 REMARK 620 6 HIS B 6 NE2 171.7 90.9 93.6 84.5 83.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MN A 601 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SRT B 1018 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SRT B 1019 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SRT A 1568 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1569 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1570 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1571 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1572 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1573 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1574 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1575 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1576 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1577 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1578 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1579 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE EDO A 1580 REMARK 999 REMARK 999 SEQUENCE REMARK 999 N-TERMINAL HISTIDINE AFFINITY TAG AND RESIDUES 18-556 ONLY. DBREF 5A29 A 19 566 UNP Q7MCK3 Q7MCK3_VIBVY 19 566 DBREF 5A29 B 0 17 PDB 5A29 5A29 0 17 SEQADV 5A29 MET A -3 UNP Q7MCK3 EXPRESSION TAG SEQADV 5A29 GLY A -2 UNP Q7MCK3 EXPRESSION TAG SEQADV 5A29 SER A -1 UNP Q7MCK3 EXPRESSION TAG SEQADV 5A29 SER A 0 UNP Q7MCK3 EXPRESSION TAG SEQADV 5A29 HIS A 1 UNP Q7MCK3 EXPRESSION TAG SEQADV 5A29 HIS A 2 UNP Q7MCK3 EXPRESSION TAG SEQADV 5A29 HIS A 3 UNP Q7MCK3 EXPRESSION TAG SEQADV 5A29 HIS A 4 UNP Q7MCK3 EXPRESSION TAG SEQADV 5A29 HIS A 5 UNP Q7MCK3 EXPRESSION TAG SEQADV 5A29 HIS A 6 UNP Q7MCK3 EXPRESSION TAG SEQADV 5A29 SER A 7 UNP Q7MCK3 EXPRESSION TAG SEQADV 5A29 SER A 8 UNP Q7MCK3 EXPRESSION TAG SEQADV 5A29 GLY A 9 UNP Q7MCK3 EXPRESSION TAG SEQADV 5A29 LEU A 10 UNP Q7MCK3 EXPRESSION TAG SEQADV 5A29 VAL A 11 UNP Q7MCK3 EXPRESSION TAG SEQADV 5A29 PRO A 12 UNP Q7MCK3 EXPRESSION TAG SEQADV 5A29 ARG A 13 UNP Q7MCK3 EXPRESSION TAG SEQADV 5A29 GLY A 14 UNP Q7MCK3 EXPRESSION TAG SEQADV 5A29 SER A 15 UNP Q7MCK3 EXPRESSION TAG SEQADV 5A29 HIS A 16 UNP Q7MCK3 EXPRESSION TAG SEQADV 5A29 ALA A 17 UNP Q7MCK3 EXPRESSION TAG SEQADV 5A29 MET A 18 UNP Q7MCK3 EXPRESSION TAG SEQRES 1 A 570 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 570 LEU VAL PRO ARG GLY SER HIS ALA MET ALA ASP TYR THR SEQRES 3 A 570 GLU GLN ASP ALA MET ARG VAL GLN ALA VAL LYS THR TYR SEQRES 4 A 570 ILE ASP ASN VAL LEU GLN GLU GLY ARG SER GLN ILE LYS SEQRES 5 A 570 THR THR PRO LEU LEU ALA ASP GLY ILE ASN THR THR THR SEQRES 6 A 570 ARG LYS PRO VAL GLU TRP ILE TYR PRO ASP GLY ARG THR SEQRES 7 A 570 ALA THR ILE SER ASN PHE ALA ASN GLN GLN ASN PHE LEU SEQRES 8 A 570 ARG ALA LEU THR ALA MET SER VAL VAL THR GLU ASP GLN SEQRES 9 A 570 ARG TYR GLN LEU GLU ALA VAL ARG ILE THR ARG TYR PHE SEQRES 10 A 570 MET ASP ASN PHE ILE ALA ASP ASN GLY LEU PHE TYR TRP SEQRES 11 A 570 GLY GLY HIS ARG PHE VAL ASN LEU ASP THR LEU GLU LEU SEQRES 12 A 570 GLU GLY PRO GLN ASN LYS ASN SER VAL HIS GLU LEU LYS SEQRES 13 A 570 ASN HIS TYR PRO TYR TYR PRO PHE LEU TYR HIS VAL ASP SEQRES 14 A 570 PRO HIS ALA THR GLU ARG TYR ILE LYS ALA PHE TRP GLN SEQRES 15 A 570 ALA HIS VAL GLU ASP TRP GLN SER LEU ASP MET GLY ARG SEQRES 16 A 570 HIS GLY SER TYR SER LYS ASN TYR ASP ASP LYS VAL PHE SEQRES 17 A 570 HIS ARG PRO ILE PRO ALA SER LEU VAL ASP GLN SER LYS SEQRES 18 A 570 LEU PRO ILE MET PRO GLU THR LYS GLY LEU THR PHE ILE SEQRES 19 A 570 ASN ALA GLY SER ASP LEU ILE TYR ALA ALA TYR GLN LEU SEQRES 20 A 570 ASP TRP LEU ALA PRO SER ALA ASN ALA GLN GLY SER ALA SEQRES 21 A 570 ALA TRP GLY GLN TYR LEU MET THR GLN TYR LYS LEU ALA SEQRES 22 A 570 LYS HIS PRO LYS THR GLY ALA PRO VAL TYR GLN PHE THR SEQRES 23 A 570 SER PRO LYS LYS ARG GLU TRP PRO PRO GLN SER ASP LYS SEQRES 24 A 570 ASP THR ASN SER LYS TYR GLY ASP ARG ALA ALA ARG GLN SEQRES 25 A 570 PHE GLY PRO GLU LEU GLY ASN ILE ALA ARG GLU GLY ASN SEQRES 26 A 570 VAL LEU PHE LYS SER ASN ASP LYS SER ILE VAL PHE ASN SEQRES 27 A 570 ASN ALA LEU ILE GLU LEU HIS LEU ALA GLU GLN ARG ASN SEQRES 28 A 570 ASP ALA ALA ILE ARG GLU GLN VAL VAL ASP ALA LEU LEU SEQRES 29 A 570 ASN PHE TYR ARG LEU ALA TYR ASN PRO GLU ASN GLY THR SEQRES 30 A 570 ILE LYS PRO ILE PHE SER ASP GLY THR SER ILE GLU GLY SEQRES 31 A 570 ILE PRO LEU ALA ARG ASP GLY TYR TYR GLY PRO LYS GLY SEQRES 32 A 570 ARG VAL PHE ASN ALA HIS LYS PRO LYS THR GLU GLU TYR SEQRES 33 A 570 LEU LEU PRO ILE LEU ARG ALA TYR ARG LEU GLN ALA ASP SEQRES 34 A 570 PRO GLU LEU TRP GLN LEU ALA ALA ASN MET THR HIS HIS SEQRES 35 A 570 TYR GLY TRP GLY SER LEU GLY ASN ASP ALA LYS ALA LYS SEQRES 36 A 570 PRO THR LEU ASN MET GLN LEU SER SER VAL SER PRO MET SEQRES 37 A 570 THR LEU PHE SER ALA ILE GLU LEU TYR GLN ILE THR GLN SEQRES 38 A 570 GLN PRO GLU TYR LEU GLU PHE ALA ARG ALA ALA ALA ASP SEQRES 39 A 570 LYS LEU VAL GLU LYS ARG PHE VAL ARG GLY TYR PHE LEU SEQRES 40 A 570 ALA ASN PRO ARG TYR LEU ASN ALA SER ILE ASP ALA ILE SEQRES 41 A 570 GLU PRO LEU ALA LEU LEU THR LEU ASP ALA THR LEU LYS SEQRES 42 A 570 GLY LYS THR ALA GLN VAL ALA PRO TYR LEU SER GLY SER SEQRES 43 A 570 GLY TYR ILE HIS GLY GLU PHE ALA GLY LYS GLU ASN ALA SEQRES 44 A 570 TYR ASP THR ASN GLU ILE TYR LYS GLN THR ARG SEQRES 1 B 18 HIS HIS HIS HIS HIS HIS HIS SER SER GLY LEU VAL PRO SEQRES 2 B 18 ARG GLY SER HIS ALA HET MN A 601 1 HET SRT A1568 10 HET EDO A1569 4 HET EDO A1570 4 HET EDO A1571 4 HET EDO A1572 4 HET EDO A1573 4 HET EDO A1574 4 HET EDO A1575 4 HET EDO A1576 4 HET EDO A1577 4 HET EDO A1578 4 HET EDO A1579 4 HET EDO A1580 4 HET SRT B1018 10 HET SRT B1019 10 HETNAM MN MANGANESE (II) ION HETNAM SRT S,R MESO-TARTARIC ACID HETNAM EDO 1,2-ETHANEDIOL HETSYN EDO ETHYLENE GLYCOL FORMUL 3 MN MN 2+ FORMUL 4 SRT 3(C4 H6 O6) FORMUL 5 EDO 12(C2 H6 O2) FORMUL 19 HOH *498(H2 O) HELIX 1 1 THR A 22 GLY A 43 1 22 HELIX 2 2 ASN A 79 ASN A 82 5 4 HELIX 3 3 GLN A 83 GLU A 98 1 16 HELIX 4 4 GLN A 100 PHE A 117 1 18 HELIX 5 5 TYR A 157 ASP A 165 1 9 HELIX 6 6 ASP A 165 VAL A 181 1 17 HELIX 7 7 LYS A 202 ARG A 206 5 5 HELIX 8 8 PHE A 229 ALA A 247 1 19 HELIX 9 9 PRO A 248 GLN A 253 1 6 HELIX 10 10 GLY A 254 ALA A 269 1 16 HELIX 11 11 ASN A 298 LYS A 300 5 3 HELIX 12 12 ASP A 303 GLY A 314 1 12 HELIX 13 13 ASN A 315 ALA A 317 5 3 HELIX 14 14 ARG A 318 ASN A 321 5 4 HELIX 15 15 SER A 326 PHE A 333 1 8 HELIX 16 16 PHE A 333 ARG A 346 1 14 HELIX 17 17 ASP A 348 TYR A 367 1 20 HELIX 18 18 TYR A 412 GLN A 423 1 12 HELIX 19 19 ASP A 425 TYR A 439 1 15 HELIX 20 20 SER A 462 GLN A 477 1 16 HELIX 21 21 PRO A 479 ARG A 496 1 18 HELIX 22 22 ILE A 516 LYS A 529 1 14 HELIX 23 23 LYS A 531 VAL A 535 5 5 HELIX 24 24 ASP A 557 ILE A 561 1 5 SHEET 1 AA 2 GLY A 56 ASN A 58 0 SHEET 2 AA 2 ASN A 510 SER A 512 -1 O ALA A 511 N ILE A 57 SHEET 1 AB 4 GLU A 66 ILE A 68 0 SHEET 2 AB 4 THR A 74 SER A 78 -1 O ALA A 75 N TRP A 67 SHEET 3 AB 4 PHE A 131 ASN A 133 -1 O VAL A 132 N SER A 78 SHEET 4 AB 4 LEU A 139 GLU A 140 -1 O GLU A 140 N PHE A 131 SHEET 1 AC 2 GLU A 223 THR A 224 0 SHEET 2 AC 2 SER A 283 PRO A 284 1 O SER A 283 N THR A 224 SHEET 1 AD 2 GLY A 442 SER A 443 0 SHEET 2 AD 2 THR A 453 LEU A 454 -1 O THR A 453 N SER A 443 SHEET 1 AE 2 PHE A 497 VAL A 498 0 SHEET 2 AE 2 TYR A 501 PHE A 502 -1 O TYR A 501 N VAL A 498 SHEET 1 AF 2 HIS A 546 PHE A 549 0 SHEET 2 AF 2 LYS A 552 TYR A 556 -1 O LYS A 552 N PHE A 549 LINK NE2 HIS A 129 MN MN A 601 1555 1555 2.12 LINK OE1 GLU A 150 MN MN A 601 1555 1555 1.99 LINK NE2 HIS A 192 MN MN A 601 1555 1555 2.10 LINK MN MN A 601 O HOH A2137 1555 1555 2.26 LINK MN MN A 601 NE2 HIS B 4 1555 1555 2.03 LINK MN MN A 601 NE2 HIS B 6 1555 1555 2.14 CISPEP 1 LEU A 218 PRO A 219 0 23.52 CISPEP 2 TRP A 289 PRO A 290 0 2.25 CISPEP 3 HIS B 0 HIS B 1 0 11.43 SITE 1 AC1 6 HIS A 129 GLU A 150 HIS A 192 HOH A2137 SITE 2 AC1 6 HIS B 4 HIS B 6 SITE 1 AC2 9 ASN A 298 SER A 299 ARG A 304 TYR A 394 SITE 2 AC2 9 HOH A2197 HOH A2487 HIS B 4 HIS B 5 SITE 3 AC2 9 HIS B 6 SITE 1 AC3 12 LYS A 152 SER A 326 LYS A 329 HOH A2240 SITE 2 AC3 12 HOH A2321 SER B 7 SER B 8 GLY B 9 SITE 3 AC3 12 LEU B 10 VAL B 11 ARG B 13 HIS B 16 SITE 1 AC4 11 ILE A 230 TYR A 266 LYS A 267 PRO A 277 SITE 2 AC4 11 VAL A 278 ILE A 331 ASN A 335 ALA A 336 SITE 3 AC4 11 GLU A 339 ALA A 358 HOH A2266 SITE 1 AC5 6 LEU A 151 PHE A 176 HIS A 180 GLY A 190 SITE 2 AC5 6 ALA A 232 HOH A2152 SITE 1 AC6 4 ARG A 418 PHE A 467 GLU A 471 GLN A 474 SITE 1 AC7 5 GLY A 190 ARG A 191 HIS A 192 HOH A2186 SITE 2 AC7 5 HOH A2487 SITE 1 AC8 7 GLN A 84 ARG A 88 HIS A 154 TYR A 155 SITE 2 AC8 7 GLY A 541 HOH A2082 HOH A2089 SITE 1 AC9 6 TYR A 508 THR A 558 TYR A 562 HOH A2488 SITE 2 AC9 6 ARG B 13 GLY B 14 SITE 1 BC1 2 PHE A 160 HOH A2159 SITE 1 BC2 4 GLN A 41 ASP A 200 LYS A 202 ARG A 206 SITE 1 BC3 6 ALA A 343 ASN A 347 ASP A 348 ALA A 349 SITE 2 BC3 6 ARG A 352 HOH A2388 SITE 1 BC4 7 LEU A 340 HIS A 341 GLU A 344 ARG A 421 SITE 2 BC4 7 PRO A 537 HOH A2326 HOH A2384 SITE 1 BC5 8 PHE A 204 HIS A 205 ARG A 206 GLY A 254 SITE 2 BC5 8 ALA A 257 HOH A2215 HOH A2259 HOH A2490 SITE 1 BC6 5 TYR A 363 TYR A 367 GLU A 427 HOH A2393 SITE 2 BC6 5 HOH A2491 SITE 1 BC7 5 SER A 443 LYS A 451 PRO A 452 THR A 453 SITE 2 BC7 5 HOH A2412 CRYST1 141.102 141.102 72.426 90.00 90.00 120.00 P 65 6 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 0.007087 0.004092 0.000000 0.00000 SCALE2 0.000000 0.008183 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013807 0.00000