HEADER TRANSFERASE 12-JUL-17 5XZA TITLE CRYSTAL STRUCTURE OF PHOSPHOFRUCTOKINASE FROM STAPHYLOCOCCUS AUREUS IN TITLE 2 COMPLEX WITH ADP COMPND MOL_ID: 1; COMPND 2 MOLECULE: ATP-DEPENDENT 6-PHOSPHOFRUCTOKINASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: PHOSPHOFRUCTOKINASE,PHOSPHOHEXOKINASE; COMPND 5 EC: 2.7.1.11; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: STAPHYLOCOCCUS AUREUS (STRAIN NCTC 8325); SOURCE 3 ORGANISM_TAXID: 93061; SOURCE 4 STRAIN: NCTC 8325; SOURCE 5 GENE: PFKA, SAOUHSC_01807; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOSPHOFRUCTOKINASE, STAPHYLOCOCCUS AUREUS, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR C.L.WANG,T.TIAN,J.Y.ZANG REVDAT 3 22-NOV-23 5XZA 1 REMARK REVDAT 2 22-MAY-19 5XZA 1 SOURCE DBREF SEQADV REVDAT 1 13-MAR-19 5XZA 0 JRNL AUTH T.TIAN,C.L.WANG,M.H.WU,X.ZHANG,J.Y.ZANG JRNL TITL STRUCTURAL INSIGHTS INTO THE REGULATION OF STAPHYLOCOCCUS JRNL TITL 2 AUREUS PHOSPHOFRUCTOKINASE BY TETRAMER-DIMER CONVERSION. JRNL REF BIOCHEMISTRY V. 57 4252 2018 JRNL REFN ISSN 1520-4995 JRNL PMID 29940104 JRNL DOI 10.1021/ACS.BIOCHEM.8B00028 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0103 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.36 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 NUMBER OF REFLECTIONS : 24166 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1253 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) : 1753 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 97.26 REMARK 3 BIN R VALUE (WORKING SET) : 0.2520 REMARK 3 BIN FREE R VALUE SET COUNT : 92 REMARK 3 BIN FREE R VALUE : 0.3280 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2423 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 46 REMARK 3 SOLVENT ATOMS : 156 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 25.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.00000 REMARK 3 B22 (A**2) : -0.03000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.02000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.156 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.144 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.110 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.765 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.952 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.929 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 2379 ; 0.019 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 2272 ; 0.007 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 3203 ; 2.058 ; 1.983 REMARK 3 BOND ANGLES OTHERS (DEGREES): 5190 ; 1.155 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 309 ; 6.227 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 94 ;35.187 ;24.894 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 390 ;16.279 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;12.971 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 372 ; 0.135 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 2698 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 501 ; 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): 1253 ; 2.504 ; 2.483 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1252 ; 2.490 ; 2.481 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1551 ; 3.404 ; 3.690 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 1552 ; 3.403 ; 3.692 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1126 ; 3.404 ; 2.901 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 1126 ; 3.402 ; 2.901 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 1653 ; 4.934 ; 4.196 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 2877 ; 6.751 ;21.526 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 2877 ; 6.750 ;21.524 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 : 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 REMARK 4 REMARK 4 5XZA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 21-JUL-17. REMARK 100 THE DEPOSITION ID IS D_1300003906. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-JUN-15 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 : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25669 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.07400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 20.8000 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) : 1.93 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.37800 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: MLPHARE REMARK 200 STARTING MODEL: 5XOE REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.33 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 15% PEG4000, 0.1M MES PH 6.0 , REMARK 280 0.15M(NH4)2SO4, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 283K 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 59.54300 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 18.40350 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 59.54300 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 18.40350 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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: 3620 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 25690 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -17.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: A REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 350 BIOMT1 2 -1.000000 0.000000 0.000000 238.17200 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 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 LEU A 323 REMARK 465 GLU A 324 REMARK 465 HIS A 325 REMARK 465 HIS A 326 REMARK 465 HIS A 327 REMARK 465 HIS A 328 REMARK 465 HIS A 329 REMARK 465 HIS A 330 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 2 CE NZ REMARK 470 ARG A 63 CG CD NE CZ NH1 NH2 REMARK 470 MET A 278 CE REMARK 470 LYS A 289 CG CD CE NZ REMARK 470 HIS A 307 CG ND1 CD2 CE1 NE2 REMARK 470 LYS A 308 CG CD CE NZ REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 LYS A 117 CG CD CE NZ REMARK 480 ARG A 164 CG CD NE CZ NH1 NH2 REMARK 480 LYS A 212 CE NZ REMARK 480 ARG A 213 NE CZ NH1 NH2 REMARK 480 LYS A 216 CD CE NZ REMARK 480 LYS A 234 CG CD CE NZ REMARK 480 GLN A 238 CG CD OE1 NE2 REMARK 480 LYS A 305 CD CE NZ REMARK 480 ASP A 306 OD1 OD2 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 CB LYS A 308 O HOH A 512 1.51 REMARK 500 O ARG A 245 O HOH A 501 1.83 REMARK 500 CE LYS A 201 OH TYR A 239 2.07 REMARK 500 CE LYS A 292 O HOH A 526 2.10 REMARK 500 OD1 ASP A 47 NH1 ARG A 92 2.18 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 526 O HOH A 592 2745 2.07 REMARK 500 O HOH A 551 O HOH A 571 2755 2.07 REMARK 500 NH2 ARG A 107 NE2 GLN A 238 4745 2.08 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 LYS A 212 C LYS A 212 O 0.140 REMARK 500 ARG A 213 C GLY A 214 N 0.199 REMARK 500 LYS A 216 C LYS A 216 O -0.331 REMARK 500 ASP A 243 CB ASP A 243 CG -0.243 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 ASP A 48 CB - CG - OD1 ANGL. DEV. = 6.4 DEGREES REMARK 500 LEU A 68 N - CA - C ANGL. DEV. = -24.7 DEGREES REMARK 500 ARG A 90 NE - CZ - NH2 ANGL. DEV. = -3.7 DEGREES REMARK 500 ARG A 107 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 GLU A 208 OE1 - CD - OE2 ANGL. DEV. = -7.5 DEGREES REMARK 500 LEU A 221 O - C - N ANGL. DEV. = -11.5 DEGREES REMARK 500 VAL A 242 CB - CA - C ANGL. DEV. = -14.3 DEGREES REMARK 500 VAL A 242 N - CA - C ANGL. DEV. = 19.7 DEGREES REMARK 500 ASP A 243 CA - CB - CG ANGL. DEV. = 17.7 DEGREES REMARK 500 ASP A 243 CB - CG - OD1 ANGL. DEV. = 12.2 DEGREES REMARK 500 ASP A 243 CB - CG - OD2 ANGL. DEV. = -12.2 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 HIS A 39 40.58 71.15 REMARK 500 TYR A 69 -167.74 -113.14 REMARK 500 ARG A 173 -114.71 53.64 REMARK 500 VAL A 242 -25.00 -142.30 REMARK 500 ARG A 245 89.09 -167.86 REMARK 500 HIS A 307 150.33 176.92 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 GLY A 304 LYS A 305 132.79 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 GLU A 208 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ADP A 401 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FLC A 402 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 403 DBREF 5XZA A 1 322 UNP Q2FXM8 PFKA_STAA8 1 322 SEQADV 5XZA LEU A 323 UNP Q2FXM8 EXPRESSION TAG SEQADV 5XZA GLU A 324 UNP Q2FXM8 EXPRESSION TAG SEQADV 5XZA HIS A 325 UNP Q2FXM8 EXPRESSION TAG SEQADV 5XZA HIS A 326 UNP Q2FXM8 EXPRESSION TAG SEQADV 5XZA HIS A 327 UNP Q2FXM8 EXPRESSION TAG SEQADV 5XZA HIS A 328 UNP Q2FXM8 EXPRESSION TAG SEQADV 5XZA HIS A 329 UNP Q2FXM8 EXPRESSION TAG SEQADV 5XZA HIS A 330 UNP Q2FXM8 EXPRESSION TAG SEQRES 1 A 330 MET LYS LYS ILE ALA VAL LEU THR SER GLY GLY ASP SER SEQRES 2 A 330 PRO GLY MET ASN ALA ALA VAL ARG ALA VAL VAL ARG THR SEQRES 3 A 330 ALA ILE TYR ASN GLU ILE GLU VAL TYR GLY VAL TYR HIS SEQRES 4 A 330 GLY TYR GLN GLY LEU LEU ASN ASP ASP ILE HIS LYS LEU SEQRES 5 A 330 GLU LEU GLY SER VAL GLY ASP THR ILE GLN ARG GLY GLY SEQRES 6 A 330 THR PHE LEU TYR SER ALA ARG CYS PRO GLU PHE LYS GLU SEQRES 7 A 330 GLN GLU VAL ARG LYS VAL ALA ILE GLU ASN LEU ARG LYS SEQRES 8 A 330 ARG GLY ILE GLU GLY LEU VAL VAL ILE GLY GLY ASP GLY SEQRES 9 A 330 SER TYR ARG GLY ALA GLN ARG ILE SER GLU GLU CYS LYS SEQRES 10 A 330 GLU ILE GLN THR ILE GLY ILE PRO GLY THR ILE ASP ASN SEQRES 11 A 330 ASP ILE ASN GLY THR ASP PHE THR ILE GLY PHE ASP THR SEQRES 12 A 330 ALA LEU ASN THR ILE ILE GLY LEU VAL ASP LYS ILE ARG SEQRES 13 A 330 ASP THR ALA SER SER HIS ALA ARG THR PHE ILE ILE GLU SEQRES 14 A 330 ALA MET GLY ARG ASP CYS GLY ASP LEU ALA LEU TRP ALA SEQRES 15 A 330 GLY LEU SER VAL GLY ALA GLU THR ILE VAL VAL PRO GLU SEQRES 16 A 330 VAL LYS THR ASP ILE LYS GLU ILE ALA ASP LYS ILE GLU SEQRES 17 A 330 GLN GLY ILE LYS ARG GLY LYS LYS HIS SER ILE VAL LEU SEQRES 18 A 330 VAL ALA GLU GLY CYS MET THR ALA GLN ASP CYS GLN LYS SEQRES 19 A 330 GLU LEU SER GLN TYR ILE ASN VAL ASP ASN ARG VAL SER SEQRES 20 A 330 VAL LEU GLY HIS VAL GLN ARG GLY GLY SER PRO THR GLY SEQRES 21 A 330 ALA ASP ARG VAL LEU ALA SER ARG LEU GLY GLY TYR ALA SEQRES 22 A 330 VAL ASP LEU LEU MET GLN GLY GLU THR ALA LYS GLY VAL SEQRES 23 A 330 GLY ILE LYS ASN ASN LYS ILE VAL ALA THR SER PHE ASP SEQRES 24 A 330 GLU ILE PHE ASP GLY LYS ASP HIS LYS PHE ASP TYR SER SEQRES 25 A 330 LEU TYR GLU LEU ALA ASN LYS LEU SER ILE LEU GLU HIS SEQRES 26 A 330 HIS HIS HIS HIS HIS HET ADP A 401 27 HET FLC A 402 13 HET GOL A 403 6 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM FLC CITRATE ANION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 FLC C6 H5 O7 3- FORMUL 4 GOL C3 H8 O3 FORMUL 5 HOH *156(H2 O) HELIX 1 AA1 GLY A 15 ASN A 30 1 16 HELIX 2 AA2 HIS A 39 ASN A 46 1 8 HELIX 3 AA3 GLU A 53 GLY A 58 5 6 HELIX 4 AA4 CYS A 73 LYS A 77 5 5 HELIX 5 AA5 GLU A 78 LYS A 91 1 14 HELIX 6 AA6 GLY A 102 CYS A 116 1 15 HELIX 7 AA7 PHE A 141 ALA A 159 1 19 HELIX 8 AA8 GLY A 176 GLY A 187 1 12 HELIX 9 AA9 ASP A 199 ARG A 213 1 15 HELIX 10 AB1 THR A 228 GLN A 238 1 11 HELIX 11 AB2 GLY A 250 GLY A 255 5 6 HELIX 12 AB3 THR A 259 GLN A 279 1 21 HELIX 13 AB4 PHE A 298 PHE A 302 1 5 HELIX 14 AB5 ASP A 310 ILE A 322 1 13 SHEET 1 AA1 6 ILE A 49 LEU A 52 0 SHEET 2 AA1 6 GLU A 33 VAL A 37 -1 N VAL A 34 O LEU A 52 SHEET 3 AA1 6 LYS A 3 THR A 8 1 N ILE A 4 O TYR A 35 SHEET 4 AA1 6 GLY A 96 GLY A 101 1 O ILE A 100 N LEU A 7 SHEET 5 AA1 6 GLN A 120 THR A 127 1 O GLN A 120 N LEU A 97 SHEET 6 AA1 6 ILE A 139 GLY A 140 1 O ILE A 139 N PRO A 125 SHEET 1 AA2 7 ILE A 49 LEU A 52 0 SHEET 2 AA2 7 GLU A 33 VAL A 37 -1 N VAL A 34 O LEU A 52 SHEET 3 AA2 7 LYS A 3 THR A 8 1 N ILE A 4 O TYR A 35 SHEET 4 AA2 7 GLY A 96 GLY A 101 1 O ILE A 100 N LEU A 7 SHEET 5 AA2 7 GLN A 120 THR A 127 1 O GLN A 120 N LEU A 97 SHEET 6 AA2 7 LYS A 284 LYS A 289 1 O VAL A 286 N GLY A 123 SHEET 7 AA2 7 LYS A 292 SER A 297 -1 O THR A 296 N GLY A 285 SHEET 1 AA3 4 THR A 190 VAL A 192 0 SHEET 2 AA3 4 SER A 218 ALA A 223 1 O LEU A 221 N THR A 190 SHEET 3 AA3 4 THR A 165 ALA A 170 1 N PHE A 166 O SER A 218 SHEET 4 AA3 4 VAL A 246 VAL A 248 1 O SER A 247 N GLU A 169 SITE 1 AC1 16 SER A 9 GLY A 10 TYR A 41 ARG A 72 SITE 2 AC1 16 CYS A 73 PHE A 76 GLY A 102 ASP A 103 SITE 3 AC1 16 GLY A 104 SER A 105 ARG A 107 GLY A 108 SITE 4 AC1 16 ARG A 111 GLN A 238 HOH A 522 HOH A 527 SITE 1 AC2 8 ARG A 21 ARG A 25 VAL A 57 GLY A 58 SITE 2 AC2 8 ASP A 59 ARG A 156 HOH A 511 HOH A 565 SITE 1 AC3 5 PHE A 137 ASP A 142 TRP A 181 ALA A 261 SITE 2 AC3 5 HOH A 505 CRYST1 119.086 36.807 89.862 90.00 124.01 90.00 C 1 2 1 4 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 0.008397 0.000000 0.005666 0.00000 SCALE2 0.000000 0.027169 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013424 0.00000