HEADER TRANSFERASE 10-JUN-04 1TMM TITLE CRYSTAL STRUCTURE OF TERNARY COMPLEX OF E.COLI HPPK(W89A) WITH TITLE 2 MGAMPCPP AND 6-HYDROXYMETHYLPTERIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-AMINO-4-HYDROXY-6-HYDROXYMETHYLDIHYDROPTERIDINE COMPND 3 PYROPHOSPHOKINASE; COMPND 4 CHAIN: A, B; COMPND 5 SYNONYM: 7,8-DIHYDRO-6-HYDROXYMETHYLPTERIN-PYROPHOSPHOKINASE, HPPK, COMPND 6 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE, PPPK; COMPND 7 EC: 2.7.6.3; COMPND 8 ENGINEERED: YES; COMPND 9 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: FOLK, B0142; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PET17B KEYWDS PYROPHOSPHOKINASE, PYROPHOSPHORYL TRANSFER, CATALYTIC MECHANISM, KEYWDS 2 FOLATE, HPPK, PTERIN, 6-HYDROXYMETHYL-7, 8-DIHYDROPTERIN, 6- KEYWDS 3 HYDROXYMETHYLPTERIN, TERNARY COMPLEX, SUBSTRATE SPECIFICITY, PRODUCT KEYWDS 4 RELEASE, ANTIMICROBIAL AGENT, DRUG DESIGN, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.BLASZCZYK,Y.LI,Y.WU,G.SHI,X.JI,H.YAN REVDAT 7 13-MAR-24 1TMM 1 COMPND SOURCE REVDAT 6 30-AUG-23 1TMM 1 AUTHOR JRNL REVDAT 5 23-AUG-23 1TMM 1 REMARK REVDAT 4 27-OCT-21 1TMM 1 REMARK SEQADV LINK REVDAT 3 13-JUL-11 1TMM 1 VERSN REVDAT 2 24-FEB-09 1TMM 1 VERSN REVDAT 1 21-JUN-05 1TMM 0 JRNL AUTH Y.LI,J.BLASZCZYK,Y.WU,G.SHI,X.JI,H.YAN JRNL TITL IS THE CRITICAL ROLE OF LOOP 3 OF ESCHERICHIA COLI JRNL TITL 2 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE IN JRNL TITL 3 CATALYSIS DUE TO LOOP-3 RESIDUES ARGININE-84 AND JRNL TITL 4 TRYPTOPHAN-89? SITE-DIRECTED MUTAGENESIS, BIOCHEMICAL, AND JRNL TITL 5 CRYSTALLOGRAPHIC STUDIES. JRNL REF BIOCHEMISTRY V. 44 8590 2005 JRNL REFN ISSN 0006-2960 JRNL PMID 15952765 JRNL DOI 10.1021/BI0503495 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH B.XIAO,G.SHI,X.CHEN,H.YAN,X.JI REMARK 1 TITL CRYSTAL STRUCTURE OF 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN REMARK 1 TITL 2 PYROPHOSPHOKINASE, A POTENTIAL TARGET FOR THE DEVELOPMENT OF REMARK 1 TITL 3 NOVEL ANTIMICROBIAL AGENTS REMARK 1 REF STRUCTURE V. 7 489 1999 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 10378268 REMARK 1 DOI 10.1016/S0969-2126(99)80065-3 REMARK 1 REFERENCE 2 REMARK 1 AUTH J.BLASZCZYK,G.SHI,H.YAN,X.JI REMARK 1 TITL CATALYTIC CENTER ASSEMBLY OF HPPK AS REVEALED BY THE CRYSTAL REMARK 1 TITL 2 STRUCTURE OF A TERNARY COMPLEX AT 1.25 A RESOLUTION REMARK 1 REF STRUCTURE V. 8 1049 2000 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 11080626 REMARK 1 DOI 10.1016/S0969-2126(00)00502-5 REMARK 1 REFERENCE 3 REMARK 1 AUTH G.SHI,J.BLASZCZYK,X.JI,H.YAN REMARK 1 TITL BISUBSTRATE ANALOGUE INHIBITORS OF REMARK 1 TITL 2 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN PYROPHOSPHOKINASE: REMARK 1 TITL 3 SYNTHESIS AND BIOCHEMICAL AND CRYSTALLOGRAPHIC STUDIES REMARK 1 REF J.MED.CHEM. V. 44 1364 2001 REMARK 1 REFN ISSN 0022-2623 REMARK 1 PMID 11311059 REMARK 1 DOI 10.1021/JM0004493 REMARK 2 REMARK 2 RESOLUTION. 1.25 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL-97 REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 4.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 CROSS-VALIDATION METHOD : FREE R REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : NULL REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.132 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.164 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 5.046 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 4128 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 81812 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : NULL REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : 0.109 REMARK 3 FREE R VALUE (F>4SIG(F)) : 0.143 REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : 5.095 REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : 3226 REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 63315 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2516 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 126 REMARK 3 SOLVENT ATOMS : 652 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : 3294.5 REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : 2430.0 REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 14 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 26939 REMARK 3 NUMBER OF RESTRAINTS : 34724 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.012 REMARK 3 ANGLE DISTANCES (A) : 0.029 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : 0.000 REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : 0.030 REMARK 3 ZERO CHIRAL VOLUMES (A**3) : 0.066 REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : 0.071 REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.089 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.005 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.053 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.090 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: NULL REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : ENGH AND HUBER REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: FULL MATRIX LEAST-SQUARES PROCEDURE, REMARK 3 WITH BLOCK OF PARAMETERS SET FOR EACH CYCLE OF INISOTROPIC REMARK 3 REFINEMENT REMARK 4 REMARK 4 1TMM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-JUL-04. REMARK 100 THE DEPOSITION ID IS D_1000022771. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-00 REMARK 200 TEMPERATURE (KELVIN) : 100.0 REMARK 200 PH : 4.60 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X9B REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97793 REMARK 200 MONOCHROMATOR : SILICON 111 REMARK 200 OPTICS : MIRROR REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 85986 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.037 REMARK 200 R MERGE (I) : 0.07800 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.47 REMARK 200 R MERGE FOR SHELL (I) : 0.60200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.000 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB 1Q0N REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 24.50 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG4000, MAGNESIUM CHLORIDE, ACETATE, REMARK 280 GLYCEROL, PH 4.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 292.0K, PH 4.60 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 23.69600 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON REMARK 300 BURIED SURFACE AREA. REMARK 350 REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS REMARK 350 GIVEN BELOW. BOTH NON-CRYSTALLOGRAPHIC AND REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN. REMARK 350 REMARK 350 BIOMOLECULE: 1 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: B REMARK 350 BIOMT1 1 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 1 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 1 0.000000 0.000000 1.000000 0.00000 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 TYR A 53 CB - CG - CD2 ANGL. DEV. = -5.6 DEGREES REMARK 500 ARG A 75 NE - CZ - NH1 ANGL. DEV. = -3.3 DEGREES REMARK 500 ARG A 75 NE - CZ - NH2 ANGL. DEV. = 7.9 DEGREES REMARK 500 ARG A 88 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 ARG A 92 NE - CZ - NH1 ANGL. DEV. = 4.7 DEGREES REMARK 500 ARG A 92 NE - CZ - NH2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG A 121 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG B 275 CD - NE - CZ ANGL. DEV. = 13.1 DEGREES REMARK 500 ARG B 275 NH1 - CZ - NH2 ANGL. DEV. = -7.7 DEGREES REMARK 500 ARG B 275 NE - CZ - NH1 ANGL. DEV. = -4.4 DEGREES REMARK 500 ARG B 275 NE - CZ - NH2 ANGL. DEV. = 12.1 DEGREES REMARK 500 ARG B 284 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 ARG B 292 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 ARG B 321 NE - CZ - NH1 ANGL. DEV. = 5.2 DEGREES REMARK 500 ARG B 344 NE - CZ - NH1 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 SER A 13 76.90 68.09 REMARK 500 ASP A 49 29.46 -68.12 REMARK 500 ALA A 151 46.59 39.91 REMARK 500 SER B 213 77.20 65.26 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 MG A 163 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLY A 26 O REMARK 620 2 SER A 31 O 103.0 REMARK 620 3 HOH A 567 O 77.6 103.8 REMARK 620 4 HOH A 644 O 103.5 94.3 161.2 REMARK 620 5 HOH A 671 O 167.5 72.9 91.7 88.7 REMARK 620 6 HOH A 672 O 92.0 164.4 83.1 78.1 93.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 161 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 95 OD1 REMARK 620 2 ASP A 97 OD1 95.0 REMARK 620 3 APC A 171 O1B 89.0 96.6 REMARK 620 4 APC A 171 O1A 93.2 169.7 89.7 REMARK 620 5 HOH A 404 O 88.3 84.6 177.1 89.4 REMARK 620 6 HOH A 408 O 176.8 84.5 94.2 86.9 88.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 162 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 95 OD2 REMARK 620 2 ASP A 97 OD2 91.2 REMARK 620 3 APC A 171 O3G 174.5 94.2 REMARK 620 4 APC A 171 O1B 90.0 97.6 89.5 REMARK 620 5 HHR A 181 O6A 85.3 170.7 89.3 91.0 REMARK 620 6 HOH A 496 O 88.1 88.8 91.8 173.4 82.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 361 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 295 OD1 REMARK 620 2 ASP B 297 OD1 92.9 REMARK 620 3 APC B 371 O1B 89.4 96.3 REMARK 620 4 APC B 371 O1A 93.8 170.9 89.9 REMARK 620 5 HOH B 431 O 89.0 84.8 178.1 89.2 REMARK 620 6 HOH B 433 O 178.2 86.0 92.2 87.2 89.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 362 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP B 295 OD2 REMARK 620 2 ASP B 297 OD2 91.6 REMARK 620 3 APC B 371 O3G 173.7 94.4 REMARK 620 4 APC B 371 O1B 88.0 99.4 89.3 REMARK 620 5 HHR B 381 O6A 86.1 169.2 88.3 91.1 REMARK 620 6 HOH B 517 O 89.8 87.6 92.2 172.7 81.8 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 MG A 161 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 162 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG A 163 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 164 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 166 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 167 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT A 168 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 361 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE MG B 362 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL B 363 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 364 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ACT B 365 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE APC A 171 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HHR A 181 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE APC B 371 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE HHR B 381 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 369 REMARK 800 REMARK 800 SITE_IDENTIFIER: BC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 170 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1HKA RELATED DB: PDB REMARK 900 1HKA IS THE CRYSTAL STRUCTURE OF APO-HPPK FROM E.COLI. REMARK 900 RELATED ID: 1EQM RELATED DB: PDB REMARK 900 1EQM IS THE CRYSTAL STRUCTURE OF BINARY COMPLEX OF HPPK FROM E.COLI REMARK 900 WITH MGADP. REMARK 900 RELATED ID: 1Q0N RELATED DB: PDB REMARK 900 1Q0N IS THE CRYSTAL STRUCTURE OF TERNARY COMPLEX OF HPPK FROM REMARK 900 E.COLI WITH MGAMPCPP AND 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN. REMARK 900 RELATED ID: 1EQ0 RELATED DB: PDB REMARK 900 1EQ0 IS THE SOLUTION STRUCTURE OF BINARY COMPLEX OF HPPK FROM REMARK 900 E.COLI WITH MGAMPPCP. REMARK 900 RELATED ID: 1EX8 RELATED DB: PDB REMARK 900 1EX8 IS THE CRYSTAL STRUCTURE OF HPPK FROM E.COLI COMPLEXED WITH REMARK 900 HP4A, A TWO-SUBSTRATE-MIMICKING INHIBITOR. REMARK 900 RELATED ID: 1CBK RELATED DB: PDB REMARK 900 1CBK IS THE CRYSTAL STRUCTURE OF BINARY COMPLEX OF HPPK FROM REMARK 900 H.INFLUENZAE WITH A 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN ANALOG. REMARK 900 RELATED ID: 1DY3 RELATED DB: PDB REMARK 900 1DY3 IS THE CRYSTAL STRUCTURE OF TERNARY COMPLEX OF HPPK FROM REMARK 900 E.COLI WITH MGATP AND A 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN ANALOG. REMARK 900 RELATED ID: 1F9Y RELATED DB: PDB REMARK 900 1F9Y IS THE CRYSTAL STRUCTURE OF TERNARY COMPLEX OF HPPK FROM REMARK 900 E.COLI WITH MGAMPCPP AND 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN ANALOGS. REMARK 900 RELATED ID: 1F9H RELATED DB: PDB REMARK 900 1F9H IS THE CRYSTAL STRUCTURE OF TERNARY COMPLEX OF HPPK(R92A) FROM REMARK 900 E.COLI WITH MGAMPCPP AND 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN. REMARK 900 RELATED ID: 1G4C RELATED DB: PDB REMARK 900 1G4C IS THE CRYSTAL STRUCTURE OF A COMPL FROM E.COLI WITH MG2+.EX REMARK 900 OF HPPK(R92A) REMARK 900 RELATED ID: 1HQ2 RELATED DB: PDB REMARK 900 1HQ2 IS THE CRYSTAL STRUCTURE OF TERNARY COMPLEX OF HPPK(R82A) FROM REMARK 900 E.COLI WITH MGAMPCPP AND 6-HYDROXYMETHYL-7,8-DIHYDROPTERIN. REMARK 900 RELATED ID: 1IM6 RELATED DB: PDB REMARK 900 1IM6 IS THE CRYSTAL STRUCTURE OF APO-HPPK(R82A) FROM E.COLI. REMARK 900 RELATED ID: 1KBR RELATED DB: PDB REMARK 900 1KBR IS THE CRYSTAL STRUCTURE OF APO-HPPK(R92A) FROM E.COLI. REMARK 900 RELATED ID: 1RU2 RELATED DB: PDB REMARK 900 1RU2 IS THE CRYSTAL STRUCTURE OF TERNARY COMPLEX OF HPPK(V83G/DEL84- REMARK 900 89) FROM E.COLI WITH MGAMPCPP AND 6-HYDROXYMETHYLPTERIN REMARK 900 (ORTHORHOMBIC FORM). REMARK 900 RELATED ID: 1RU1 RELATED DB: PDB REMARK 900 1RU1 IS THE CRYSTAL STRUCTURE OF TERNARY COMPLEX OF HPPK(V83G/DEL84- REMARK 900 89) FROM E.COLI WITH MGAMPCPP AND 6-HYDROXYMETHYLPTERIN (MONOCLINIC REMARK 900 FORM). REMARK 900 RELATED ID: 1RTZ RELATED DB: PDB REMARK 900 1RTZ IS THE CRYSTAL STRUCTURE OF APO-HPPK(V83G/DEL84-89) FROM REMARK 900 E.COLI. REMARK 900 RELATED ID: 1RB0 RELATED DB: PDB REMARK 900 1RB0 IS THE CRYSTAL STRUCTURE OF BINARY COMPLEX OF HPPK FROM E.COLI REMARK 900 WITH 6-HYDROXYMETHYLPTERIN-DIPHOSPHATE. REMARK 900 RELATED ID: 1TMJ RELATED DB: PDB REMARK 900 1TMJ IS THE CRYSTAL STRUCTURE OF APO-HPPK(W89A) FROM E.COLI. DBREF 1TMM A 1 158 UNP P26281 HPPK_ECOLI 1 158 DBREF 1TMM B 201 358 UNP P26281 HPPK_ECOLI 1 158 SEQADV 1TMM ALA A 89 UNP P26281 TRP 89 ENGINEERED MUTATION SEQADV 1TMM ALA B 289 UNP P26281 TRP 89 ENGINEERED MUTATION SEQRES 1 A 158 THR VAL ALA TYR ILE ALA ILE GLY SER ASN LEU ALA SER SEQRES 2 A 158 PRO LEU GLU GLN VAL ASN ALA ALA LEU LYS ALA LEU GLY SEQRES 3 A 158 ASP ILE PRO GLU SER HIS ILE LEU THR VAL SER SER PHE SEQRES 4 A 158 TYR ARG THR PRO PRO LEU GLY PRO GLN ASP GLN PRO ASP SEQRES 5 A 158 TYR LEU ASN ALA ALA VAL ALA LEU GLU THR SER LEU ALA SEQRES 6 A 158 PRO GLU GLU LEU LEU ASN HIS THR GLN ARG ILE GLU LEU SEQRES 7 A 158 GLN GLN GLY ARG VAL ARG LYS ALA GLU ARG ALA GLY PRO SEQRES 8 A 158 ARG THR LEU ASP LEU ASP ILE MET LEU PHE GLY ASN GLU SEQRES 9 A 158 VAL ILE ASN THR GLU ARG LEU THR VAL PRO HIS TYR ASP SEQRES 10 A 158 MET LYS ASN ARG GLY PHE MET LEU TRP PRO LEU PHE GLU SEQRES 11 A 158 ILE ALA PRO GLU LEU VAL PHE PRO ASP GLY GLU MET LEU SEQRES 12 A 158 ARG GLN ILE LEU HIS THR ARG ALA PHE ASP LYS LEU ASN SEQRES 13 A 158 LYS TRP SEQRES 1 B 158 THR VAL ALA TYR ILE ALA ILE GLY SER ASN LEU ALA SER SEQRES 2 B 158 PRO LEU GLU GLN VAL ASN ALA ALA LEU LYS ALA LEU GLY SEQRES 3 B 158 ASP ILE PRO GLU SER HIS ILE LEU THR VAL SER SER PHE SEQRES 4 B 158 TYR ARG THR PRO PRO LEU GLY PRO GLN ASP GLN PRO ASP SEQRES 5 B 158 TYR LEU ASN ALA ALA VAL ALA LEU GLU THR SER LEU ALA SEQRES 6 B 158 PRO GLU GLU LEU LEU ASN HIS THR GLN ARG ILE GLU LEU SEQRES 7 B 158 GLN GLN GLY ARG VAL ARG LYS ALA GLU ARG ALA GLY PRO SEQRES 8 B 158 ARG THR LEU ASP LEU ASP ILE MET LEU PHE GLY ASN GLU SEQRES 9 B 158 VAL ILE ASN THR GLU ARG LEU THR VAL PRO HIS TYR ASP SEQRES 10 B 158 MET LYS ASN ARG GLY PHE MET LEU TRP PRO LEU PHE GLU SEQRES 11 B 158 ILE ALA PRO GLU LEU VAL PHE PRO ASP GLY GLU MET LEU SEQRES 12 B 158 ARG GLN ILE LEU HIS THR ARG ALA PHE ASP LYS LEU ASN SEQRES 13 B 158 LYS TRP HET MG A 161 1 HET MG A 162 1 HET MG A 163 1 HET CL A 164 1 HET ACT A 166 4 HET ACT A 167 4 HET ACT A 168 4 HET CL A 364 1 HET APC A 171 31 HET HHR A 181 14 HET GOL A 170 6 HET MG B 361 1 HET MG B 362 1 HET CL B 363 1 HET ACT B 365 4 HET APC B 371 31 HET HHR B 381 14 HET GOL B 369 6 HETNAM MG MAGNESIUM ION HETNAM CL CHLORIDE ION HETNAM ACT ACETATE ION HETNAM APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER HETNAM HHR 6-HYDROXYMETHYLPTERIN HETNAM GOL GLYCEROL HETSYN APC ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 MG 5(MG 2+) FORMUL 6 CL 3(CL 1-) FORMUL 7 ACT 4(C2 H3 O2 1-) FORMUL 11 APC 2(C11 H18 N5 O12 P3) FORMUL 12 HHR 2(C7 H7 N5 O2) FORMUL 13 GOL 2(C3 H8 O3) FORMUL 21 HOH *652(H2 O) HELIX 1 1 SER A 13 ASP A 27 1 15 HELIX 2 2 ALA A 65 GLN A 80 1 16 HELIX 3 3 ASP A 117 ASN A 120 5 4 HELIX 4 4 ARG A 121 ALA A 132 1 12 HELIX 5 5 MET A 142 ARG A 150 1 9 HELIX 6 6 SER B 213 ASP B 227 1 15 HELIX 7 7 ALA B 265 GLN B 280 1 16 HELIX 8 8 ASP B 317 ASN B 320 5 4 HELIX 9 9 ARG B 321 ALA B 332 1 12 HELIX 10 10 MET B 342 ALA B 351 1 10 SHEET 1 A 4 SER A 31 VAL A 36 0 SHEET 2 A 4 TYR A 53 THR A 62 -1 O ALA A 59 N LEU A 34 SHEET 3 A 4 VAL A 2 SER A 9 -1 N ALA A 3 O LEU A 60 SHEET 4 A 4 ASP A 95 PHE A 101 -1 O ASP A 97 N ALA A 6 SHEET 1 B 4 SER A 31 VAL A 36 0 SHEET 2 B 4 TYR A 53 THR A 62 -1 O ALA A 59 N LEU A 34 SHEET 3 B 4 TYR A 40 THR A 42 -1 N THR A 42 O TYR A 53 SHEET 4 B 4 ASN A 156 LYS A 157 -1 O ASN A 156 N ARG A 41 SHEET 1 C 2 ILE A 106 ASN A 107 0 SHEET 2 C 2 THR A 112 VAL A 113 -1 O VAL A 113 N ILE A 106 SHEET 1 D 4 SER B 231 VAL B 236 0 SHEET 2 D 4 TYR B 253 THR B 262 -1 O GLU B 261 N HIS B 232 SHEET 3 D 4 VAL B 202 SER B 209 -1 N ALA B 203 O LEU B 260 SHEET 4 D 4 ASP B 295 PHE B 301 -1 O ASP B 297 N ALA B 206 SHEET 1 E 4 SER B 231 VAL B 236 0 SHEET 2 E 4 TYR B 253 THR B 262 -1 O GLU B 261 N HIS B 232 SHEET 3 E 4 TYR B 240 THR B 242 -1 N THR B 242 O TYR B 253 SHEET 4 E 4 ASN B 356 LYS B 357 -1 O ASN B 356 N ARG B 241 SHEET 1 F 2 ILE B 306 ASN B 307 0 SHEET 2 F 2 THR B 312 VAL B 313 -1 O VAL B 313 N ILE B 306 LINK O GLY A 26 MG MG A 163 1555 1555 2.38 LINK O SER A 31 MG MG A 163 1555 1555 2.28 LINK OD1 ASP A 95 MG MG A 161 1555 1555 2.06 LINK OD2 ASP A 95 MG MG A 162 1555 1555 2.09 LINK OD1 ASP A 97 MG MG A 161 1555 1555 2.05 LINK OD2 ASP A 97 MG MG A 162 1555 1555 2.02 LINK MG MG A 161 O1B APC A 171 1555 1555 2.09 LINK MG MG A 161 O1A APC A 171 1555 1555 2.11 LINK MG MG A 161 O HOH A 404 1555 1555 2.08 LINK MG MG A 161 O HOH A 408 1555 1555 2.08 LINK MG MG A 162 O3G APC A 171 1555 1555 2.02 LINK MG MG A 162 O1B APC A 171 1555 1555 2.14 LINK MG MG A 162 O6A HHR A 181 1555 1555 2.14 LINK MG MG A 162 O HOH A 496 1555 1555 2.10 LINK MG MG A 163 O HOH A 567 1555 1555 2.45 LINK MG MG A 163 O HOH A 644 1555 1555 2.21 LINK MG MG A 163 O HOH A 671 1555 1555 2.60 LINK MG MG A 163 O HOH A 672 1555 1555 2.60 LINK OD1 ASP B 295 MG MG B 361 1555 1555 2.09 LINK OD2 ASP B 295 MG MG B 362 1555 1555 2.10 LINK OD1 ASP B 297 MG MG B 361 1555 1555 2.04 LINK OD2 ASP B 297 MG MG B 362 1555 1555 1.96 LINK MG MG B 361 O1B APC B 371 1555 1555 2.07 LINK MG MG B 361 O1A APC B 371 1555 1555 2.08 LINK MG MG B 361 O HOH B 431 1555 1555 2.07 LINK MG MG B 361 O HOH B 433 1555 1555 2.09 LINK MG MG B 362 O3G APC B 371 1555 1555 2.04 LINK MG MG B 362 O1B APC B 371 1555 1555 2.16 LINK MG MG B 362 O6A HHR B 381 1555 1555 2.17 LINK MG MG B 362 O HOH B 517 1555 1555 2.17 CISPEP 1 VAL A 113 PRO A 114 0 -9.05 CISPEP 2 VAL B 313 PRO B 314 0 -8.82 SITE 1 AC1 6 ASP A 95 ASP A 97 MG A 162 APC A 171 SITE 2 AC1 6 HOH A 404 HOH A 408 SITE 1 AC2 6 ASP A 95 ASP A 97 MG A 161 APC A 171 SITE 2 AC2 6 HHR A 181 HOH A 496 SITE 1 AC3 6 GLY A 26 SER A 31 HOH A 567 HOH A 644 SITE 2 AC3 6 HOH A 671 HOH A 672 SITE 1 AC4 5 LYS A 119 PHE A 137 PRO A 138 ASP A 139 SITE 2 AC4 5 HOH A 688 SITE 1 AC5 2 HIS A 148 THR A 149 SITE 1 AC6 6 GLU A 30 SER A 31 HIS A 32 HOH A 480 SITE 2 AC6 6 HOH A 671 HOH A 819 SITE 1 AC7 4 LYS A 119 GOL A 170 HOH A 417 HOH A 771 SITE 1 AC8 6 ASP B 295 ASP B 297 MG B 362 APC B 371 SITE 2 AC8 6 HOH B 431 HOH B 433 SITE 1 AC9 6 ASP B 295 ASP B 297 MG B 361 APC B 371 SITE 2 AC9 6 HHR B 381 HOH B 517 SITE 1 BC1 4 LYS B 319 PHE B 337 ASP B 339 HOH B 525 SITE 1 BC2 4 VAL A 83 ARG A 84 HOH A 503 HOH A 643 SITE 1 BC3 6 ASN A 107 PRO B 266 GLU B 304 HOH B 603 SITE 2 BC3 6 HOH B 624 HOH B 714 SITE 1 BC4 28 GLN A 74 ARG A 82 LYS A 85 ALA A 86 SITE 2 BC4 28 ARG A 92 ASP A 95 ASP A 97 ILE A 98 SITE 3 BC4 28 ARG A 110 LEU A 111 THR A 112 HIS A 115 SITE 4 BC4 28 TYR A 116 ARG A 121 MG A 161 MG A 162 SITE 5 BC4 28 HHR A 181 HOH A 404 HOH A 408 HOH A 435 SITE 6 BC4 28 HOH A 440 HOH A 460 HOH A 496 HOH A 575 SITE 7 BC4 28 HOH A 584 HOH A 601 HOH A 627 HOH A 805 SITE 1 BC5 14 THR A 42 PRO A 43 PRO A 44 LEU A 45 SITE 2 BC5 14 TYR A 53 ASN A 55 ASP A 95 PHE A 123 SITE 3 BC5 14 MG A 162 APC A 171 HOH A 407 HOH A 469 SITE 4 BC5 14 HOH A 496 HOH A 616 SITE 1 BC6 30 LEU B 270 GLN B 274 ARG B 282 LYS B 285 SITE 2 BC6 30 ALA B 286 ARG B 292 ASP B 295 ASP B 297 SITE 3 BC6 30 ILE B 298 ARG B 310 LEU B 311 THR B 312 SITE 4 BC6 30 HIS B 315 TYR B 316 ARG B 321 MG B 361 SITE 5 BC6 30 MG B 362 HHR B 381 HOH B 431 HOH B 433 SITE 6 BC6 30 HOH B 436 HOH B 449 HOH B 471 HOH B 473 SITE 7 BC6 30 HOH B 507 HOH B 517 HOH B 576 HOH B 605 SITE 8 BC6 30 HOH B 670 HOH B 889 SITE 1 BC7 13 THR B 242 PRO B 243 LEU B 245 TYR B 253 SITE 2 BC7 13 ASN B 255 ARG B 292 ASP B 295 PHE B 323 SITE 3 BC7 13 MG B 362 APC B 371 HOH B 464 HOH B 499 SITE 4 BC7 13 HOH B 517 SITE 1 BC8 8 GLN B 274 LEU B 278 LYS B 285 HOH B 432 SITE 2 BC8 8 HOH B 578 HOH B 654 HOH B 670 HOH B 804 SITE 1 BC9 5 THR A 112 TYR A 116 ACT A 168 HOH A 409 SITE 2 BC9 5 HOH A 920 CRYST1 47.992 47.392 71.438 90.00 104.13 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 0.020837 0.000000 0.005245 0.00000 SCALE2 0.000000 0.021101 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014435 0.00000