PDB Short entry for 3DRW HEADER TRANSFERASE 11-JUL-08 3DRW TITLE CRYSTAL STRUCTURE OF A PHOSPHOFRUCTOKINASE FROM PYROCOCCUS HORIKOSHII TITLE 2 OT3 WITH AMP COMPND MOL_ID: 1; COMPND 2 MOLECULE: ADP-SPECIFIC PHOSPHOFRUCTOKINASE; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: PHOSPHOFRUCTOKINASE; COMPND 5 SYNONYM: ADP-DEPENDENT PHOSPHOFRUCTOKINASE, ADP-PFK; COMPND 6 EC: 2.7.1.146; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PYROCOCCUS HORIKOSHII; SOURCE 3 ORGANISM_TAXID: 53953; SOURCE 4 STRAIN: OT3; SOURCE 5 GENE: PFKC, PH1645; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS 6-PHOSPHOFRUCTOKINASE, PYROCOCCUS HORIKOSHII, AMP, ADP, GLYCOLYSIS, KEYWDS 2 KINASE, MAGNESIUM, METAL-BINDING, TRANSFERASE, STRUCTURAL GENOMICS, KEYWDS 3 PSI-2, PROTEIN STRUCTURE INITIATIVE, MIDWEST CENTER FOR STRUCTURAL KEYWDS 4 GENOMICS, MCSG EXPDTA X-RAY DIFFRACTION AUTHOR A.U.SINGER,T.SKARINA,S.KOCHINYAN,G.BROWN,M.E.CUFF,A.M.EDWARDS, AUTHOR 2 A.JOACHIMIAK,A.SAVCHENKO,A.F.YAKUNIN,Z.JIA,MIDWEST CENTER FOR AUTHOR 3 STRUCTURAL GENOMICS (MCSG) REVDAT 4 30-AUG-23 3DRW 1 REMARK REVDAT 3 20-OCT-21 3DRW 1 REMARK SEQADV REVDAT 2 17-OCT-12 3DRW 1 JRNL VERSN REVDAT 1 23-DEC-08 3DRW 0 JRNL AUTH M.A.CURRIE,F.MERINO,T.SKARINA,A.H.WONG,A.SINGER,G.BROWN, JRNL AUTH 2 A.SAVCHENKO,A.CANIUGUIR,V.GUIXE,A.F.YAKUNIN,Z.JIA JRNL TITL ADP-DEPENDENT 6-PHOSPHOFRUCTOKINASE FROM PYROCOCCUS JRNL TITL 2 HORIKOSHII OT3: STRUCTURE DETERMINATION AND BIOCHEMICAL JRNL TITL 3 CHARACTERIZATION OF PH1645. JRNL REF J.BIOL.CHEM. V. 284 22664 2009 JRNL REFN ISSN 0021-9258 JRNL PMID 19553681 JRNL DOI 10.1074/JBC.M109.012401 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 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) : 41.45 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 71005 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) : 0.174 REMARK 3 R VALUE (WORKING SET) : 0.172 REMARK 3 FREE R VALUE : 0.224 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3770 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) : 1.94 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4513 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.03 REMARK 3 BIN R VALUE (WORKING SET) : 0.2100 REMARK 3 BIN FREE R VALUE SET COUNT : 224 REMARK 3 BIN FREE R VALUE : 0.3050 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 7379 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 576 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 23.50 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.05000 REMARK 3 B22 (A**2) : 0.10000 REMARK 3 B33 (A**2) : -0.04000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.03000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.151 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.146 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.102 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 6.497 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.965 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 7600 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 10267 ; 1.800 ; 1.989 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 915 ; 7.542 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 366 ;33.107 ;23.579 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 1401 ;15.637 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 66 ;18.377 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 1141 ; 0.165 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 5711 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 3544 ; 0.220 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 5297 ; 0.316 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 504 ; 0.150 ; 0.200 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): 108 ; 0.215 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 27 ; 0.153 ; 0.200 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): 4550 ; 1.082 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 7376 ; 1.991 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 3108 ; 3.545 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 2890 ; 5.917 ; 4.500 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 REMARK 4 REMARK 4 3DRW COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 11-AUG-08. REMARK 100 THE DEPOSITION ID IS D_1000048410. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 24-OCT-07 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 : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97929 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTAL REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 74815 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.7 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : 0.08000 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 16.7000 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) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.35300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 3.200 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: 1U2X MOLECULE A REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.05 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 3350, 0.2 M LITHIUM CITRATE REMARK 280 PLUS 5 MM ADP CRYOPROTECTED IN N-PARATONE OIL., VAPOR DIFFUSION, REMARK 280 HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 52.09500 REMARK 290 SMTRY3 2 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: 3910 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 38410 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -23.0 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 -21 REMARK 465 GLY A -20 REMARK 465 SER A -19 REMARK 465 SER A -18 REMARK 465 HIS A -17 REMARK 465 HIS A -16 REMARK 465 HIS A -15 REMARK 465 HIS A -14 REMARK 465 HIS A -13 REMARK 465 HIS A -12 REMARK 465 SER A -11 REMARK 465 HIS A 0 REMARK 465 GLY A 451 REMARK 465 SER A 452 REMARK 465 MET B -21 REMARK 465 GLY B -20 REMARK 465 SER B -19 REMARK 465 SER B -18 REMARK 465 HIS B -17 REMARK 465 HIS B -16 REMARK 465 HIS B -15 REMARK 465 HIS B -14 REMARK 465 HIS B -13 REMARK 465 HIS B -12 REMARK 465 SER B -11 REMARK 465 SER B -10 REMARK 465 GLY B -9 REMARK 465 ARG B -8 REMARK 465 GLU B -7 REMARK 465 ASN B -6 REMARK 465 LEU B -5 REMARK 465 TYR B -4 REMARK 465 PHE B -3 REMARK 465 GLN B -2 REMARK 465 GLY B -1 REMARK 465 HIS B 0 REMARK 465 GLY B 451 REMARK 465 SER B 452 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 ARG A -8 CG CD NE CZ NH1 NH2 REMARK 470 TYR A -4 CG CD1 CD2 CE1 CE2 CZ OH 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 OE2 GLU B 330 OH TYR B 443 2.17 REMARK 500 O3P AMP B 1485 O HOH B 1785 2.19 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 ARG A -8 5.91 83.67 REMARK 500 TYR A 46 69.79 63.49 REMARK 500 ASN A 139 54.42 71.20 REMARK 500 ASP A 175 51.76 -118.41 REMARK 500 ARG A 191 38.97 -146.04 REMARK 500 GLN A 265 -73.73 -26.30 REMARK 500 PHE A 329 -167.29 -77.02 REMARK 500 TYR B 46 73.97 60.74 REMARK 500 ASP B 282 -62.47 -101.32 REMARK 500 TYR B 300 61.53 -106.75 REMARK 500 ARG B 410 -139.28 49.68 REMARK 500 ASN B 424 78.88 -118.47 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 AMP A 1484 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1485 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA A 1486 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE AMP B 1485 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1U2X RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A HYPOTHETICAL ADP-DEPENDENT REMARK 900 PHOSPHOFRUCTOKINASE FROM PYROCOCCUS HORIKOSHII OT3 REMARK 900 RELATED ID: APC5054 RELATED DB: TARGETDB DBREF 3DRW A 1 450 UNP O59355 K6PF_PYRHO 1 450 DBREF 3DRW B 1 450 UNP O59355 K6PF_PYRHO 1 450 SEQADV 3DRW MET A -21 UNP O59355 EXPRESSION TAG SEQADV 3DRW GLY A -20 UNP O59355 EXPRESSION TAG SEQADV 3DRW SER A -19 UNP O59355 EXPRESSION TAG SEQADV 3DRW SER A -18 UNP O59355 EXPRESSION TAG SEQADV 3DRW HIS A -17 UNP O59355 EXPRESSION TAG SEQADV 3DRW HIS A -16 UNP O59355 EXPRESSION TAG SEQADV 3DRW HIS A -15 UNP O59355 EXPRESSION TAG SEQADV 3DRW HIS A -14 UNP O59355 EXPRESSION TAG SEQADV 3DRW HIS A -13 UNP O59355 EXPRESSION TAG SEQADV 3DRW HIS A -12 UNP O59355 EXPRESSION TAG SEQADV 3DRW SER A -11 UNP O59355 EXPRESSION TAG SEQADV 3DRW SER A -10 UNP O59355 EXPRESSION TAG SEQADV 3DRW GLY A -9 UNP O59355 EXPRESSION TAG SEQADV 3DRW ARG A -8 UNP O59355 EXPRESSION TAG SEQADV 3DRW GLU A -7 UNP O59355 EXPRESSION TAG SEQADV 3DRW ASN A -6 UNP O59355 EXPRESSION TAG SEQADV 3DRW LEU A -5 UNP O59355 EXPRESSION TAG SEQADV 3DRW TYR A -4 UNP O59355 EXPRESSION TAG SEQADV 3DRW PHE A -3 UNP O59355 EXPRESSION TAG SEQADV 3DRW GLN A -2 UNP O59355 EXPRESSION TAG SEQADV 3DRW GLY A -1 UNP O59355 EXPRESSION TAG SEQADV 3DRW HIS A 0 UNP O59355 EXPRESSION TAG SEQADV 3DRW ALA A 17 UNP O59355 ASP 17 ENGINEERED MUTATION SEQADV 3DRW GLY A 451 UNP O59355 EXPRESSION TAG SEQADV 3DRW SER A 452 UNP O59355 EXPRESSION TAG SEQADV 3DRW MET B -21 UNP O59355 EXPRESSION TAG SEQADV 3DRW GLY B -20 UNP O59355 EXPRESSION TAG SEQADV 3DRW SER B -19 UNP O59355 EXPRESSION TAG SEQADV 3DRW SER B -18 UNP O59355 EXPRESSION TAG SEQADV 3DRW HIS B -17 UNP O59355 EXPRESSION TAG SEQADV 3DRW HIS B -16 UNP O59355 EXPRESSION TAG SEQADV 3DRW HIS B -15 UNP O59355 EXPRESSION TAG SEQADV 3DRW HIS B -14 UNP O59355 EXPRESSION TAG SEQADV 3DRW HIS B -13 UNP O59355 EXPRESSION TAG SEQADV 3DRW HIS B -12 UNP O59355 EXPRESSION TAG SEQADV 3DRW SER B -11 UNP O59355 EXPRESSION TAG SEQADV 3DRW SER B -10 UNP O59355 EXPRESSION TAG SEQADV 3DRW GLY B -9 UNP O59355 EXPRESSION TAG SEQADV 3DRW ARG B -8 UNP O59355 EXPRESSION TAG SEQADV 3DRW GLU B -7 UNP O59355 EXPRESSION TAG SEQADV 3DRW ASN B -6 UNP O59355 EXPRESSION TAG SEQADV 3DRW LEU B -5 UNP O59355 EXPRESSION TAG SEQADV 3DRW TYR B -4 UNP O59355 EXPRESSION TAG SEQADV 3DRW PHE B -3 UNP O59355 EXPRESSION TAG SEQADV 3DRW GLN B -2 UNP O59355 EXPRESSION TAG SEQADV 3DRW GLY B -1 UNP O59355 EXPRESSION TAG SEQADV 3DRW HIS B 0 UNP O59355 EXPRESSION TAG SEQADV 3DRW ALA B 17 UNP O59355 ASP 17 ENGINEERED MUTATION SEQADV 3DRW GLY B 451 UNP O59355 EXPRESSION TAG SEQADV 3DRW SER B 452 UNP O59355 EXPRESSION TAG SEQRES 1 A 474 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 A 474 ARG GLU ASN LEU TYR PHE GLN GLY HIS MET ILE PRO GLU SEQRES 3 A 474 HIS LEU SER ILE TYR THR ALA TYR ASN ALA ASN ILE ALA SEQRES 4 A 474 ALA ILE VAL LYS LEU ASN GLN GLU THR ILE GLN ASN LEU SEQRES 5 A 474 ILE ASN ALA PHE ASP PRO ASP GLU VAL LYS ARG ARG ILE SEQRES 6 A 474 GLU GLU TYR PRO ARG GLU ILE ASN GLU PRO ILE ASP PHE SEQRES 7 A 474 VAL ALA ARG LEU VAL HIS THR LEU LYS LEU GLY LYS PRO SEQRES 8 A 474 ALA ALA VAL PRO LEU VAL ASN GLU LYS MET ASN GLU TRP SEQRES 9 A 474 PHE ASP LYS THR PHE ARG TYR GLU GLU GLU ARG LEU GLY SEQRES 10 A 474 GLY GLN ALA GLY ILE ILE ALA ASN THR LEU ALA GLY LEU SEQRES 11 A 474 LYS ILE ARG LYS VAL ILE ALA TYR THR PRO PHE LEU PRO SEQRES 12 A 474 LYS ARG LEU ALA GLU LEU PHE LYS LYS GLY VAL LEU TYR SEQRES 13 A 474 PRO VAL VAL GLU ASN GLY GLU LEU GLN PHE LYS PRO ILE SEQRES 14 A 474 GLN GLU ALA TYR ARG GLU GLY ASP PRO LEU LYS ILE ASN SEQRES 15 A 474 ARG ILE PHE GLU PHE ARG LYS GLY LEU LYS PHE LYS LEU SEQRES 16 A 474 GLY ASP GLU THR ILE GLU ILE PRO ASN SER GLY ARG PHE SEQRES 17 A 474 ILE VAL SER ALA ARG PHE GLU SER ILE SER ARG ILE GLU SEQRES 18 A 474 THR ARG GLU ASP ILE LYS PRO PHE LEU GLY GLU ILE GLY SEQRES 19 A 474 LYS GLU VAL ASP GLY ALA ILE PHE SER GLY TYR GLN GLY SEQRES 20 A 474 LEU ARG THR LYS TYR SER ASP GLY LYS ASP ALA ASN TYR SEQRES 21 A 474 TYR LEU ARG ARG ALA LYS GLU ASP ILE ILE GLU PHE LYS SEQRES 22 A 474 GLU LYS ASP VAL LYS ILE HIS VAL GLU PHE ALA SER VAL SEQRES 23 A 474 GLN ASP ARG LYS LEU ARG LYS LYS ILE ILE THR ASN ILE SEQRES 24 A 474 LEU PRO PHE VAL ASP SER VAL GLY ILE ASP GLU ALA GLU SEQRES 25 A 474 ILE ALA GLN ILE LEU SER VAL LEU GLY TYR ARG GLU LEU SEQRES 26 A 474 ALA ASP ARG ILE PHE THR TYR ASN ARG LEU GLU ASP SER SEQRES 27 A 474 ILE LEU GLY GLY MET ILE ILE LEU ASP GLU LEU ASN PHE SEQRES 28 A 474 GLU ILE LEU GLN VAL HIS THR THR TYR TYR LEU MET TYR SEQRES 29 A 474 ILE THR HIS ARG ASP ASN PRO LEU SER GLU GLU GLU LEU SEQRES 30 A 474 ALA LYS SER LEU GLU PHE GLY THR THR LEU ALA ALA ALA SEQRES 31 A 474 ARG ALA SER LEU GLY ASP ILE ARG GLY PRO ASP ASP TYR SEQRES 32 A 474 LYS VAL GLY LEU LYS VAL PRO PHE ASN GLU ARG SER GLU SEQRES 33 A 474 TYR VAL LYS LEU ARG PHE GLU GLU ALA LYS SER ARG LEU SEQRES 34 A 474 ARG MET ARG GLU TYR LYS VAL VAL VAL ILE PRO THR ARG SEQRES 35 A 474 LEU VAL GLN ASN PRO VAL LEU THR VAL GLY LEU GLY ASP SEQRES 36 A 474 THR ILE SER ALA GLY ALA PHE LEU THR TYR LEU GLU PHE SEQRES 37 A 474 LEU LYS ARG HIS GLY SER SEQRES 1 B 474 MET GLY SER SER HIS HIS HIS HIS HIS HIS SER SER GLY SEQRES 2 B 474 ARG GLU ASN LEU TYR PHE GLN GLY HIS MET ILE PRO GLU SEQRES 3 B 474 HIS LEU SER ILE TYR THR ALA TYR ASN ALA ASN ILE ALA SEQRES 4 B 474 ALA ILE VAL LYS LEU ASN GLN GLU THR ILE GLN ASN LEU SEQRES 5 B 474 ILE ASN ALA PHE ASP PRO ASP GLU VAL LYS ARG ARG ILE SEQRES 6 B 474 GLU GLU TYR PRO ARG GLU ILE ASN GLU PRO ILE ASP PHE SEQRES 7 B 474 VAL ALA ARG LEU VAL HIS THR LEU LYS LEU GLY LYS PRO SEQRES 8 B 474 ALA ALA VAL PRO LEU VAL ASN GLU LYS MET ASN GLU TRP SEQRES 9 B 474 PHE ASP LYS THR PHE ARG TYR GLU GLU GLU ARG LEU GLY SEQRES 10 B 474 GLY GLN ALA GLY ILE ILE ALA ASN THR LEU ALA GLY LEU SEQRES 11 B 474 LYS ILE ARG LYS VAL ILE ALA TYR THR PRO PHE LEU PRO SEQRES 12 B 474 LYS ARG LEU ALA GLU LEU PHE LYS LYS GLY VAL LEU TYR SEQRES 13 B 474 PRO VAL VAL GLU ASN GLY GLU LEU GLN PHE LYS PRO ILE SEQRES 14 B 474 GLN GLU ALA TYR ARG GLU GLY ASP PRO LEU LYS ILE ASN SEQRES 15 B 474 ARG ILE PHE GLU PHE ARG LYS GLY LEU LYS PHE LYS LEU SEQRES 16 B 474 GLY ASP GLU THR ILE GLU ILE PRO ASN SER GLY ARG PHE SEQRES 17 B 474 ILE VAL SER ALA ARG PHE GLU SER ILE SER ARG ILE GLU SEQRES 18 B 474 THR ARG GLU ASP ILE LYS PRO PHE LEU GLY GLU ILE GLY SEQRES 19 B 474 LYS GLU VAL ASP GLY ALA ILE PHE SER GLY TYR GLN GLY SEQRES 20 B 474 LEU ARG THR LYS TYR SER ASP GLY LYS ASP ALA ASN TYR SEQRES 21 B 474 TYR LEU ARG ARG ALA LYS GLU ASP ILE ILE GLU PHE LYS SEQRES 22 B 474 GLU LYS ASP VAL LYS ILE HIS VAL GLU PHE ALA SER VAL SEQRES 23 B 474 GLN ASP ARG LYS LEU ARG LYS LYS ILE ILE THR ASN ILE SEQRES 24 B 474 LEU PRO PHE VAL ASP SER VAL GLY ILE ASP GLU ALA GLU SEQRES 25 B 474 ILE ALA GLN ILE LEU SER VAL LEU GLY TYR ARG GLU LEU SEQRES 26 B 474 ALA ASP ARG ILE PHE THR TYR ASN ARG LEU GLU ASP SER SEQRES 27 B 474 ILE LEU GLY GLY MET ILE ILE LEU ASP GLU LEU ASN PHE SEQRES 28 B 474 GLU ILE LEU GLN VAL HIS THR THR TYR TYR LEU MET TYR SEQRES 29 B 474 ILE THR HIS ARG ASP ASN PRO LEU SER GLU GLU GLU LEU SEQRES 30 B 474 ALA LYS SER LEU GLU PHE GLY THR THR LEU ALA ALA ALA SEQRES 31 B 474 ARG ALA SER LEU GLY ASP ILE ARG GLY PRO ASP ASP TYR SEQRES 32 B 474 LYS VAL GLY LEU LYS VAL PRO PHE ASN GLU ARG SER GLU SEQRES 33 B 474 TYR VAL LYS LEU ARG PHE GLU GLU ALA LYS SER ARG LEU SEQRES 34 B 474 ARG MET ARG GLU TYR LYS VAL VAL VAL ILE PRO THR ARG SEQRES 35 B 474 LEU VAL GLN ASN PRO VAL LEU THR VAL GLY LEU GLY ASP SEQRES 36 B 474 THR ILE SER ALA GLY ALA PHE LEU THR TYR LEU GLU PHE SEQRES 37 B 474 LEU LYS ARG HIS GLY SER HET AMP A1484 23 HET NA A1485 1 HET NA A1486 1 HET AMP B1485 23 HETNAM AMP ADENOSINE MONOPHOSPHATE HETNAM NA SODIUM ION FORMUL 3 AMP 2(C10 H14 N5 O7 P) FORMUL 4 NA 2(NA 1+) FORMUL 7 HOH *576(H2 O) HELIX 1 1 ASN A 23 ALA A 33 1 11 HELIX 2 2 ASP A 35 TYR A 46 1 12 HELIX 3 3 GLU A 52 GLY A 67 1 16 HELIX 4 4 LYS A 78 PHE A 87 1 10 HELIX 5 5 GLY A 96 LEU A 108 1 13 HELIX 6 6 PRO A 121 GLU A 126 1 6 HELIX 7 7 GLN A 148 ALA A 150 5 3 HELIX 8 8 GLU A 193 ARG A 197 5 5 HELIX 9 9 ILE A 204 PRO A 206 5 3 HELIX 10 10 PHE A 207 VAL A 215 1 9 HELIX 11 11 GLY A 222 LEU A 226 5 5 HELIX 12 12 ASP A 235 LYS A 253 1 19 HELIX 13 13 ASP A 266 ILE A 277 1 12 HELIX 14 14 LEU A 278 VAL A 281 5 4 HELIX 15 15 GLU A 288 GLY A 299 1 12 HELIX 16 16 TYR A 300 ASN A 311 1 12 HELIX 17 17 ARG A 312 ASN A 328 1 17 HELIX 18 18 SER A 351 GLY A 373 1 23 HELIX 19 19 GLY A 377 ASP A 379 5 3 HELIX 20 20 ASP A 380 LYS A 386 1 7 HELIX 21 21 ARG A 392 LEU A 407 1 16 HELIX 22 22 GLY A 430 LYS A 448 1 19 HELIX 23 23 ASN B 23 ALA B 33 1 11 HELIX 24 24 ASP B 35 TYR B 46 1 12 HELIX 25 25 GLU B 52 GLY B 67 1 16 HELIX 26 26 LYS B 78 PHE B 87 1 10 HELIX 27 27 GLY B 96 LEU B 108 1 13 HELIX 28 28 PRO B 121 GLU B 126 1 6 HELIX 29 29 GLN B 148 ALA B 150 5 3 HELIX 30 30 GLU B 193 ARG B 197 5 5 HELIX 31 31 ILE B 204 PRO B 206 5 3 HELIX 32 32 PHE B 207 VAL B 215 1 9 HELIX 33 33 GLY B 222 LEU B 226 5 5 HELIX 34 34 ASP B 235 LYS B 253 1 19 HELIX 35 35 ASP B 266 LEU B 278 1 13 HELIX 36 36 PRO B 279 VAL B 281 5 3 HELIX 37 37 GLU B 288 LEU B 298 1 11 HELIX 38 38 TYR B 300 ASN B 311 1 12 HELIX 39 39 ARG B 312 ASN B 328 1 17 HELIX 40 40 SER B 351 GLY B 373 1 23 HELIX 41 41 GLY B 377 ASP B 379 5 3 HELIX 42 42 ASP B 380 LEU B 385 1 6 HELIX 43 43 ARG B 392 LEU B 407 1 16 HELIX 44 44 GLY B 430 LYS B 448 1 19 SHEET 1 A10 LEU A 142 PRO A 146 0 SHEET 2 A10 VAL A 132 VAL A 137 -1 N VAL A 136 O GLN A 143 SHEET 3 A10 LYS A 112 ALA A 115 1 N VAL A 113 O LEU A 133 SHEET 4 A10 SER A 7 ALA A 11 1 N ILE A 8 O ILE A 114 SHEET 5 A10 GLY A 217 PHE A 220 1 O GLY A 217 N TYR A 9 SHEET 6 A10 LYS A 256 GLU A 260 1 O HIS A 258 N PHE A 220 SHEET 7 A10 SER A 283 ASP A 287 1 O SER A 283 N VAL A 259 SHEET 8 A10 ILE A 331 HIS A 335 1 O GLN A 333 N VAL A 284 SHEET 9 A10 TYR A 339 HIS A 345 -1 O ILE A 343 N LEU A 332 SHEET 10 A10 TYR A 412 PRO A 418 -1 O ILE A 417 N LEU A 340 SHEET 1 B 5 ALA A 70 LEU A 74 0 SHEET 2 B 5 GLY A 184 ALA A 190 1 O SER A 189 N LEU A 74 SHEET 3 B 5 ILE A 159 PHE A 165 -1 N PHE A 163 O PHE A 186 SHEET 4 B 5 ASN A 15 LYS A 21 1 N ALA A 18 O ASN A 160 SHEET 5 B 5 GLU A 91 GLY A 95 -1 O ARG A 93 N ALA A 17 SHEET 1 C 2 LYS A 170 LYS A 172 0 SHEET 2 C 2 THR A 177 GLU A 179 -1 O ILE A 178 N PHE A 171 SHEET 1 D10 GLU B 141 PRO B 146 0 SHEET 2 D10 VAL B 132 GLU B 138 -1 N GLU B 138 O GLU B 141 SHEET 3 D10 LYS B 112 TYR B 116 1 N ALA B 115 O LEU B 133 SHEET 4 D10 SER B 7 ALA B 11 1 N ILE B 8 O ILE B 114 SHEET 5 D10 GLY B 217 PHE B 220 1 O ILE B 219 N TYR B 9 SHEET 6 D10 LYS B 256 GLU B 260 1 O HIS B 258 N PHE B 220 SHEET 7 D10 SER B 283 ASP B 287 1 O SER B 283 N VAL B 259 SHEET 8 D10 ILE B 331 HIS B 335 1 O GLN B 333 N VAL B 284 SHEET 9 D10 TYR B 339 THR B 344 -1 O ILE B 343 N LEU B 332 SHEET 10 D10 LYS B 413 PRO B 418 -1 O ILE B 417 N LEU B 340 SHEET 1 E 5 ALA B 70 LEU B 74 0 SHEET 2 E 5 GLY B 184 ALA B 190 1 O SER B 189 N LEU B 74 SHEET 3 E 5 ILE B 159 PHE B 165 -1 N ARG B 161 O VAL B 188 SHEET 4 E 5 ASN B 15 LYS B 21 1 N VAL B 20 O ILE B 162 SHEET 5 E 5 GLU B 91 GLY B 95 -1 O GLY B 95 N ASN B 15 SHEET 1 F 2 LYS B 170 LEU B 173 0 SHEET 2 F 2 GLU B 176 GLU B 179 -1 O ILE B 178 N PHE B 171 CISPEP 1 ALA A 11 TYR A 12 0 9.37 CISPEP 2 ALA B 11 TYR B 12 0 11.37 SITE 1 AC1 11 THR A 336 THR A 337 ARG A 420 LEU A 421 SITE 2 AC1 11 VAL A 422 LEU A 431 ILE A 435 NA A1486 SITE 3 AC1 11 HOH A1641 HOH A1656 HOH A1730 SITE 1 AC2 3 THR A 104 ARG A 369 ILE A 375 SITE 1 AC3 3 LEU A 431 GLY A 432 AMP A1484 SITE 1 AC4 12 HIS B 335 THR B 336 THR B 337 THR B 419 SITE 2 AC4 12 ARG B 420 LEU B 421 VAL B 422 LEU B 431 SITE 3 AC4 12 GLY B 432 ILE B 435 HOH B1707 HOH B1785 CRYST1 68.464 104.190 70.844 90.00 105.09 90.00 P 1 21 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 0.014606 0.000000 0.003938 0.00000 SCALE2 0.000000 0.009598 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014620 0.00000