HEADER LYASE 08-AUG-23 8Q57 TITLE CRYSTAL STRUCTURE OF CLASS II SFP ALDOLASE FROM YERSINIA ALDOVAE TITLE 2 (YASQIA-ZN-SO4) WITH BOUND SULFATE IONS COMPND MOL_ID: 1; COMPND 2 MOLECULE: TAGATOSE-1,6-BISPHOSPHATE ALDOLASE KBAY; COMPND 3 CHAIN: A, B; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: YERSINIA ALDOVAE; SOURCE 3 ORGANISM_TAXID: 29483; SOURCE 4 GENE: KBAY; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS METAL-DEPENDENT, ALDOLASE, SULFOQUINOVOSE, SULFOFRUCTOSE PHOSPHATE, KEYWDS 2 LYASE EXPDTA X-RAY DIFFRACTION AUTHOR M.SHARMA,G.J.DAVIES REVDAT 3 22-NOV-23 8Q57 1 JRNL REVDAT 2 01-NOV-23 8Q57 1 REMARK REVDAT 1 25-OCT-23 8Q57 0 JRNL AUTH M.SHARMA,A.KAUR,N.MADIEDO SOLER,J.P.LINGFORD,R.EPA, JRNL AUTH 2 E.D.GODDARD-BORGER,G.J.DAVIES,S.J.WILLIAMS JRNL TITL DEFINING THE MOLECULAR ARCHITECTURE, METAL DEPENDENCE, AND JRNL TITL 2 DISTRIBUTION OF METAL-DEPENDENT CLASS II JRNL TITL 3 SULFOFRUCTOSE-1-PHOSPHATE ALDOLASES. JRNL REF J.BIOL.CHEM. V. 299 05338 2023 JRNL REFN ESSN 1083-351X JRNL PMID 37838169 JRNL DOI 10.1016/J.JBC.2023.105338 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0419 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) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 61.01 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 81063 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) : 0.186 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 4241 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) : 1.70 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.74 REMARK 3 REFLECTION IN BIN (WORKING SET) : 5995 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.92 REMARK 3 BIN R VALUE (WORKING SET) : 0.2890 REMARK 3 BIN FREE R VALUE SET COUNT : 308 REMARK 3 BIN FREE R VALUE : 0.2820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4181 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 68 REMARK 3 SOLVENT ATOMS : 271 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.01 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -1.35000 REMARK 3 B22 (A**2) : -1.26000 REMARK 3 B33 (A**2) : 2.14000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.06000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.086 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.084 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.069 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 2.230 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.959 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4355 ; 0.010 ; 0.012 REMARK 3 BOND LENGTHS OTHERS (A): 4168 ; 0.001 ; 0.016 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5900 ; 1.511 ; 1.645 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9563 ; 0.520 ; 1.568 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 567 ; 5.730 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 23 ; 9.819 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 716 ;13.320 ;10.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 690 ; 0.083 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5097 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 959 ; 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): 2236 ; 2.846 ; 2.828 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2236 ; 2.843 ; 2.827 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2792 ; 3.619 ; 5.055 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2793 ; 3.618 ; 5.056 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2119 ; 3.892 ; 3.212 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2120 ; 3.891 ; 3.214 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 3101 ; 5.652 ; 5.740 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 4831 ; 6.851 ;30.500 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4832 ; 6.850 ;30.500 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 REMARK 4 REMARK 4 8Q57 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 08-AUG-23. REMARK 100 THE DEPOSITION ID IS D_1292131360. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JAN-20 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 : DIAMOND REMARK 200 BEAMLINE : I04 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 : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 85319 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.700 REMARK 200 RESOLUTION RANGE LOW (A) : 61.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 7.100 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.70 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.73 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : 6.90 REMARK 200 R MERGE FOR SHELL (I) : 1.18100 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 60.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.08 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PROTEIN AT 16 MG ML-1 IN 50 MM NAPI, REMARK 280 300 MM NACL BUFFER PH 7.4, USING A DROP CONTAINING 0.6 UL REMARK 280 PROTEIN AND 0.5 UL MOTHER LIQUOR, THE LATTER COMPRISING 1.5 M REMARK 280 AMMONIUM SULFATE, 0.1 M NACL, 0.1 M BIS-TRIS PH 6.5, VAPOR REMARK 280 DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 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+1/2 REMARK 290 4555 -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 29.48384 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 43.76250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 49.67870 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 29.48384 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 43.76250 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 49.67870 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: TETRAMERIC 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 58.96768 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 99.35741 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 434 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 425 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 MET A -19 REMARK 465 GLY A -18 REMARK 465 SER A -17 REMARK 465 SER A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 HIS A -11 REMARK 465 HIS A -10 REMARK 465 SER A -9 REMARK 465 SER A -8 REMARK 465 GLY A -7 REMARK 465 LEU A -6 REMARK 465 VAL A -5 REMARK 465 PRO A -4 REMARK 465 ARG A -3 REMARK 465 GLY A -2 REMARK 465 SER A -1 REMARK 465 HIS A 0 REMARK 465 ASP A 143 REMARK 465 ASP A 144 REMARK 465 ILE A 145 REMARK 465 SER A 146 REMARK 465 VAL A 147 REMARK 465 ASP A 148 REMARK 465 GLU A 149 REMARK 465 LYS A 150 REMARK 465 ASP A 151 REMARK 465 ALA A 152 REMARK 465 MET B -19 REMARK 465 GLY B -18 REMARK 465 SER B -17 REMARK 465 SER B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 HIS B -11 REMARK 465 HIS B -10 REMARK 465 SER B -9 REMARK 465 SER B -8 REMARK 465 GLY B -7 REMARK 465 LEU B -6 REMARK 465 VAL B -5 REMARK 465 PRO B -4 REMARK 465 ARG B -3 REMARK 465 GLY B -2 REMARK 465 SER B -1 REMARK 465 HIS B 0 REMARK 465 ASP B 143 REMARK 465 ASP B 144 REMARK 465 ILE B 145 REMARK 465 SER B 146 REMARK 465 VAL B 147 REMARK 465 ASP B 148 REMARK 465 GLU B 149 REMARK 465 LYS B 150 REMARK 465 ASP B 151 REMARK 465 ALA B 152 REMARK 465 ALA B 288 REMARK 465 GLY B 289 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 MET A 1 CG SD CE REMARK 470 LYS A 60 CD CE NZ REMARK 470 ARG A 85 NE CZ NH1 NH2 REMARK 470 LYS A 137 CE NZ REMARK 470 GLU A 142 CG CD OE1 OE2 REMARK 470 LEU A 153 CG CD1 CD2 REMARK 470 LYS A 162 NZ REMARK 470 GLU A 165 CD OE1 OE2 REMARK 470 LYS A 184 CG CD CE NZ REMARK 470 GLN A 185 CG CD OE1 NE2 REMARK 470 LYS A 188 CD CE NZ REMARK 470 GLU A 192 CG CD OE1 OE2 REMARK 470 LYS B 60 CD CE NZ REMARK 470 GLU B 142 CG CD OE1 OE2 REMARK 470 LEU B 153 CG CD1 CD2 REMARK 470 LYS B 162 NZ REMARK 470 LYS B 184 CG CD CE NZ REMARK 470 GLN B 185 CG CD OE1 NE2 REMARK 470 LYS B 188 CG CD CE NZ REMARK 470 GLU B 216 CD OE1 OE2 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 64 CD GLU B 64 OE2 -0.079 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 27 -168.04 -174.84 REMARK 500 ILE A 176 25.43 -141.31 REMARK 500 ASP A 232 -65.37 -128.63 REMARK 500 ASN B 27 -166.68 -173.34 REMARK 500 ASP B 232 -65.20 -130.43 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ARG A 198 0.14 SIDE CHAIN REMARK 500 ARG A 264 0.08 SIDE CHAIN REMARK 500 ARG B 198 0.09 SIDE CHAIN REMARK 500 ARG B 264 0.09 SIDE CHAIN 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 ZN A 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 83 NE2 REMARK 620 2 HIS A 180 NE2 109.9 REMARK 620 3 HIS A 180 NE2 91.4 26.2 REMARK 620 4 HIS A 208 ND1 106.3 143.0 159.2 REMARK 620 5 HOH A 492 O 106.7 78.2 101.1 84.6 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 304 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 83 NE2 REMARK 620 2 HIS A 180 NE2 77.9 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 305 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 179 O REMARK 620 2 GLY A 181 O 106.5 REMARK 620 3 SER A 211 O 138.5 101.4 REMARK 620 4 SO4 A 302 O2 98.3 117.0 95.6 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 303 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS B 83 NE2 REMARK 620 2 HIS B 180 NE2 112.5 REMARK 620 3 HIS B 180 NE2 105.8 27.5 REMARK 620 4 HIS B 208 ND1 104.1 140.6 147.2 REMARK 620 5 HOH B 471 O 102.1 73.3 100.7 85.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 305 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 179 O REMARK 620 2 GLY B 181 O 106.3 REMARK 620 3 SER B 211 O 138.1 99.8 REMARK 620 4 SO4 B 301 O4 104.2 116.3 92.4 REMARK 620 N 1 2 3 DBREF1 8Q57 A 1 289 UNP A0A0T9TPS2_YERAL DBREF2 8Q57 A A0A0T9TPS2 1 289 DBREF1 8Q57 B 1 289 UNP A0A0T9TPS2_YERAL DBREF2 8Q57 B A0A0T9TPS2 1 289 SEQADV 8Q57 MET A -19 UNP A0A0T9TPS INITIATING METHIONINE SEQADV 8Q57 GLY A -18 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 SER A -17 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 SER A -16 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 HIS A -15 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 HIS A -14 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 HIS A -13 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 HIS A -12 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 HIS A -11 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 HIS A -10 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 SER A -9 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 SER A -8 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 GLY A -7 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 LEU A -6 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 VAL A -5 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 PRO A -4 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 ARG A -3 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 GLY A -2 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 SER A -1 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 HIS A 0 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 GLN A 40 UNP A0A0T9TPS GLU 40 CONFLICT SEQADV 8Q57 ALA A 288 UNP A0A0T9TPS VAL 288 CONFLICT SEQADV 8Q57 MET B -19 UNP A0A0T9TPS INITIATING METHIONINE SEQADV 8Q57 GLY B -18 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 SER B -17 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 SER B -16 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 HIS B -15 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 HIS B -14 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 HIS B -13 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 HIS B -12 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 HIS B -11 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 HIS B -10 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 SER B -9 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 SER B -8 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 GLY B -7 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 LEU B -6 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 VAL B -5 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 PRO B -4 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 ARG B -3 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 GLY B -2 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 SER B -1 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 HIS B 0 UNP A0A0T9TPS EXPRESSION TAG SEQADV 8Q57 GLN B 40 UNP A0A0T9TPS GLU 40 CONFLICT SEQADV 8Q57 ALA B 288 UNP A0A0T9TPS VAL 288 CONFLICT SEQRES 1 A 309 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 309 LEU VAL PRO ARG GLY SER HIS MET SER TYR VAL SER GLY SEQRES 3 A 309 ASN THR LEU ILE GLN HIS ALA TRP GLN HIS GLY TYR ALA SEQRES 4 A 309 ILE GLY ALA PHE SER VAL HIS ASN ALA GLU THR ILE ARG SEQRES 5 A 309 ALA ILE LEU LEU ALA ALA GLU GLN GLU GLN ALA PRO VAL SEQRES 6 A 309 MET LEU GLN ILE GLY GLN LYS VAL ILE SER VAL MET GLY SEQRES 7 A 309 LEU LYS PRO MET LYS GLU MET ILE ASP ALA PHE MET HIS SEQRES 8 A 309 ASP ILE THR VAL PRO VAL CYS ILE HIS LEU ASP HIS SER SEQRES 9 A 309 ARG SER PHE GLU GLN THR MET GLU ALA VAL GLN ALA GLY SEQRES 10 A 309 PHE GLN SER VAL MET PHE ASP GLY SER HIS LEU SER PHE SEQRES 11 A 309 ASP GLU ASN VAL ARG ILE THR ARG ALA VAL ALA ASP VAL SEQRES 12 A 309 ALA HIS ALA LEU ASN LEU GLY VAL GLU GLY GLU ILE GLY SEQRES 13 A 309 LYS ILE GLY GLY THR GLU ASP ASP ILE SER VAL ASP GLU SEQRES 14 A 309 LYS ASP ALA LEU ILE THR SER CYS ALA GLU ALA LEU LYS SEQRES 15 A 309 PHE SER GLU LEU THR THR VAL ASP TYR LEU ALA VAL SER SEQRES 16 A 309 ILE GLY THR ALA HIS GLY MET TYR LYS GLN GLU PRO LYS SEQRES 17 A 309 LEU ALA PHE GLU ARG LEU GLN GLU MET ARG GLU ILE VAL SEQRES 18 A 309 LYS LYS PRO ILE VAL LEU HIS GLY GLY SER GLY VAL PRO SEQRES 19 A 309 ASP GLU GLN ILE ARG ARG ALA ILE THR LEU GLY VAL ALA SEQRES 20 A 309 LYS VAL ASN VAL ASP THR GLU LEU ARG GLN ALA PHE THR SEQRES 21 A 309 GLN GLY VAL SER GLU VAL LEU ALA ALA SER PRO ASP GLU SEQRES 22 A 309 TYR VAL LEU ALA VAL SER LEU GLY ARG GLY ARG ASP VAL SEQRES 23 A 309 MET GLN GLN LYS VAL ILE GLU LYS ILE ARG LEU PHE GLY SEQRES 24 A 309 SER GLN GLY GLN ALA ALA ALA PHE ALA GLY SEQRES 1 B 309 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 309 LEU VAL PRO ARG GLY SER HIS MET SER TYR VAL SER GLY SEQRES 3 B 309 ASN THR LEU ILE GLN HIS ALA TRP GLN HIS GLY TYR ALA SEQRES 4 B 309 ILE GLY ALA PHE SER VAL HIS ASN ALA GLU THR ILE ARG SEQRES 5 B 309 ALA ILE LEU LEU ALA ALA GLU GLN GLU GLN ALA PRO VAL SEQRES 6 B 309 MET LEU GLN ILE GLY GLN LYS VAL ILE SER VAL MET GLY SEQRES 7 B 309 LEU LYS PRO MET LYS GLU MET ILE ASP ALA PHE MET HIS SEQRES 8 B 309 ASP ILE THR VAL PRO VAL CYS ILE HIS LEU ASP HIS SER SEQRES 9 B 309 ARG SER PHE GLU GLN THR MET GLU ALA VAL GLN ALA GLY SEQRES 10 B 309 PHE GLN SER VAL MET PHE ASP GLY SER HIS LEU SER PHE SEQRES 11 B 309 ASP GLU ASN VAL ARG ILE THR ARG ALA VAL ALA ASP VAL SEQRES 12 B 309 ALA HIS ALA LEU ASN LEU GLY VAL GLU GLY GLU ILE GLY SEQRES 13 B 309 LYS ILE GLY GLY THR GLU ASP ASP ILE SER VAL ASP GLU SEQRES 14 B 309 LYS ASP ALA LEU ILE THR SER CYS ALA GLU ALA LEU LYS SEQRES 15 B 309 PHE SER GLU LEU THR THR VAL ASP TYR LEU ALA VAL SER SEQRES 16 B 309 ILE GLY THR ALA HIS GLY MET TYR LYS GLN GLU PRO LYS SEQRES 17 B 309 LEU ALA PHE GLU ARG LEU GLN GLU MET ARG GLU ILE VAL SEQRES 18 B 309 LYS LYS PRO ILE VAL LEU HIS GLY GLY SER GLY VAL PRO SEQRES 19 B 309 ASP GLU GLN ILE ARG ARG ALA ILE THR LEU GLY VAL ALA SEQRES 20 B 309 LYS VAL ASN VAL ASP THR GLU LEU ARG GLN ALA PHE THR SEQRES 21 B 309 GLN GLY VAL SER GLU VAL LEU ALA ALA SER PRO ASP GLU SEQRES 22 B 309 TYR VAL LEU ALA VAL SER LEU GLY ARG GLY ARG ASP VAL SEQRES 23 B 309 MET GLN GLN LYS VAL ILE GLU LYS ILE ARG LEU PHE GLY SEQRES 24 B 309 SER GLN GLY GLN ALA ALA ALA PHE ALA GLY HET SO4 A 301 5 HET SO4 A 302 5 HET ZN A 303 1 HET ZN A 304 1 HET NA A 305 1 HET BTB A 306 14 HET BTB A 307 14 HET SO4 B 301 5 HET SO4 B 302 5 HET ZN B 303 1 HET ZN B 304 1 HET NA B 305 1 HET BTB B 306 14 HETNAM SO4 SULFATE ION HETNAM ZN ZINC ION HETNAM NA SODIUM ION HETNAM BTB 2-[BIS-(2-HYDROXY-ETHYL)-AMINO]-2-HYDROXYMETHYL- HETNAM 2 BTB PROPANE-1,3-DIOL HETSYN BTB BIS-TRIS BUFFER FORMUL 3 SO4 4(O4 S 2-) FORMUL 5 ZN 4(ZN 2+) FORMUL 7 NA 2(NA 1+) FORMUL 8 BTB 3(C8 H19 N O5) FORMUL 16 HOH *271(H2 O) HELIX 1 AA1 SER A 5 HIS A 16 1 12 HELIX 2 AA2 ASN A 27 GLN A 42 1 16 HELIX 3 AA3 GLY A 50 GLY A 58 1 9 HELIX 4 AA4 GLY A 58 PHE A 69 1 12 HELIX 5 AA5 SER A 86 ALA A 96 1 11 HELIX 6 AA6 SER A 109 LEU A 127 1 19 HELIX 7 AA7 SER A 156 THR A 168 1 13 HELIX 8 AA8 ALA A 190 VAL A 201 1 12 HELIX 9 AA9 PRO A 214 LEU A 224 1 11 HELIX 10 AB1 ASP A 232 SER A 250 1 19 HELIX 11 AB2 VAL A 255 PHE A 278 1 24 HELIX 12 AB3 ALA A 284 GLY A 289 1 6 HELIX 13 AB4 SER B 5 GLY B 17 1 13 HELIX 14 AB5 ASN B 27 GLN B 42 1 16 HELIX 15 AB6 GLY B 50 GLY B 58 1 9 HELIX 16 AB7 GLY B 58 MET B 70 1 13 HELIX 17 AB8 SER B 86 ALA B 96 1 11 HELIX 18 AB9 SER B 109 LEU B 127 1 19 HELIX 19 AC1 SER B 156 THR B 168 1 13 HELIX 20 AC2 ALA B 190 VAL B 201 1 12 HELIX 21 AC3 PRO B 214 LEU B 224 1 11 HELIX 22 AC4 ASP B 232 SER B 250 1 19 HELIX 23 AC5 VAL B 255 PHE B 278 1 24 HELIX 24 AC6 GLY B 282 PHE B 287 5 6 SHEET 1 AA1 9 ILE A 20 SER A 24 0 SHEET 2 AA1 9 VAL A 45 ILE A 49 1 O MET A 46 N PHE A 23 SHEET 3 AA1 9 VAL A 77 SER A 84 1 O HIS A 80 N ILE A 49 SHEET 4 AA1 9 SER A 100 PHE A 103 1 O MET A 102 N LEU A 81 SHEET 5 AA1 9 GLY A 130 ILE A 135 1 O GLU A 132 N VAL A 101 SHEET 6 AA1 9 TYR A 171 VAL A 174 1 O ALA A 173 N GLY A 133 SHEET 7 AA1 9 ILE A 205 LEU A 207 1 O VAL A 206 N LEU A 172 SHEET 8 AA1 9 VAL A 226 VAL A 231 1 O LYS A 228 N LEU A 207 SHEET 9 AA1 9 ILE A 20 SER A 24 1 N ILE A 20 O ALA A 227 SHEET 1 AA2 9 ILE B 20 SER B 24 0 SHEET 2 AA2 9 VAL B 45 ILE B 49 1 O MET B 46 N PHE B 23 SHEET 3 AA2 9 VAL B 77 SER B 84 1 O HIS B 80 N ILE B 49 SHEET 4 AA2 9 SER B 100 PHE B 103 1 O MET B 102 N LEU B 81 SHEET 5 AA2 9 GLY B 130 ILE B 135 1 O GLU B 132 N VAL B 101 SHEET 6 AA2 9 TYR B 171 VAL B 174 1 O ALA B 173 N GLY B 133 SHEET 7 AA2 9 ILE B 205 LEU B 207 1 O VAL B 206 N LEU B 172 SHEET 8 AA2 9 VAL B 226 VAL B 231 1 O LYS B 228 N LEU B 207 SHEET 9 AA2 9 ILE B 20 SER B 24 1 N ALA B 22 O VAL B 229 LINK NE2 HIS A 83 ZN ZN A 303 1555 1555 2.11 LINK NE2 HIS A 83 ZN ZN A 304 1555 1555 2.68 LINK O ALA A 179 NA NA A 305 1555 1555 2.83 LINK NE2AHIS A 180 ZN ZN A 303 1555 1555 2.00 LINK NE2BHIS A 180 ZN ZN A 303 1555 1555 2.53 LINK NE2BHIS A 180 ZN ZN A 304 1555 1555 2.62 LINK O GLY A 181 NA NA A 305 1555 1555 2.62 LINK ND1 HIS A 208 ZN ZN A 303 1555 1555 1.87 LINK O SER A 211 NA NA A 305 1555 1555 2.89 LINK O2 SO4 A 302 NA NA A 305 1555 1555 2.81 LINK ZN ZN A 303 O HOH A 492 1555 1555 2.65 LINK NE2 HIS B 83 ZN ZN B 303 1555 1555 2.11 LINK O ALA B 179 NA NA B 305 1555 1555 2.80 LINK NE2AHIS B 180 ZN ZN B 303 1555 1555 1.92 LINK NE2BHIS B 180 ZN ZN B 303 1555 1555 2.46 LINK NE2BHIS B 180 ZN ZN B 304 1555 1555 2.52 LINK O GLY B 181 NA NA B 305 1555 1555 2.72 LINK ND1 HIS B 208 ZN ZN B 303 1555 1555 1.94 LINK O SER B 211 NA NA B 305 1555 1555 2.99 LINK O4 SO4 B 301 NA NA B 305 1555 1555 2.85 LINK ZN ZN B 303 O HOH B 471 1555 1555 2.69 CRYST1 90.734 87.525 104.312 90.00 107.73 90.00 I 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 0.011021 0.000000 0.003524 0.00000 SCALE2 0.000000 0.011425 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010065 0.00000