HEADER TRANSFERASE 27-MAR-15 4Z1D TITLE STRUCTURE OF PEP AND ZINC BOUND KDO8PS FROM H.PYLORI COMPND MOL_ID: 1; COMPND 2 MOLECULE: 2-DEHYDRO-3-DEOXYPHOSPHOOCTONATE ALDOLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: 3-DEOXY-D-MANNO-OCTULOSONIC ACID 8-PHOSPHATE SYNTHASE,KDO-8- COMPND 5 PHOSPHATE SYNTHASE,KDOPS,PHOSPHO-2-DEHYDRO-3-DEOXYOCTONATE ALDOLASE; COMPND 6 EC: 2.5.1.55; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HELICOBACTER PYLORI (STRAIN ATCC 700392 / SOURCE 3 26695); SOURCE 4 ORGANISM_TAXID: 85962; SOURCE 5 STRAIN: ATCC 700392 / 26695; SOURCE 6 GENE: KDSA, HP_0003; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PCOLD I KEYWDS HELICOBACTER PYLORI, LIPOPOLYSACCHARIDE BIOSYNTHESIS, LIGAND BOUND, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR B.J.LEE,S.CHO,H.IM,H.J.YOON REVDAT 3 20-MAR-24 4Z1D 1 REMARK REVDAT 2 19-FEB-20 4Z1D 1 JRNL REMARK REVDAT 1 09-MAR-16 4Z1D 0 JRNL AUTH S.CHO,H.IM,K.Y.LEE,J.CHEN,H.J.KANG,H.J.YOON,K.H.MIN,K.R.LEE, JRNL AUTH 2 H.J.PARK,B.J.LEE JRNL TITL IDENTIFICATION OF NOVEL SCAFFOLDS FOR POTENTIAL JRNL TITL 2 ANTI-HELICOBACTER PYLORI AGENTS BASED ON THE CRYSTAL JRNL TITL 3 STRUCTURE OF H. PYLORI 3-DEOXY-D-MANNO-OCTULOSONATE JRNL TITL 4 8-PHOSPHATE SYNTHASE (HPKDO8PS). JRNL REF EUR.J.MED.CHEM. V. 108 188 2016 JRNL REFN ISSN 0223-5234 JRNL PMID 26649906 JRNL DOI 10.1016/J.EJMECH.2015.11.036 REMARK 2 REMARK 2 RESOLUTION. 1.65 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.8.0049 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) : 1.65 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 3 NUMBER OF REFLECTIONS : 61335 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.186 REMARK 3 FREE R VALUE : 0.212 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 3276 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) : 1.65 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.69 REMARK 3 REFLECTION IN BIN (WORKING SET) : 3870 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.47 REMARK 3 BIN R VALUE (WORKING SET) : 0.2190 REMARK 3 BIN FREE R VALUE SET COUNT : 229 REMARK 3 BIN FREE R VALUE : 0.2530 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3990 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 22 REMARK 3 SOLVENT ATOMS : 595 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.13 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.01000 REMARK 3 B22 (A**2) : -0.01000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.01000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.103 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.098 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.066 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.900 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.949 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4074 ; 0.006 ; 0.019 REMARK 3 BOND LENGTHS OTHERS (A): 4000 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5502 ; 1.185 ; 1.983 REMARK 3 BOND ANGLES OTHERS (DEGREES): 9216 ; 0.720 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 508 ; 5.849 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 174 ;36.721 ;25.057 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 746 ;11.785 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 20 ;16.492 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 632 ; 0.065 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4558 ; 0.004 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 878 ; 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): 2044 ; 0.824 ; 1.785 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 2043 ; 0.822 ; 1.784 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 2548 ; 1.382 ; 2.670 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): 2549 ; 1.382 ; 2.671 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2030 ; 1.180 ; 1.976 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): 2029 ; 1.179 ; 1.976 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): 2954 ; 1.936 ; 2.897 REMARK 3 LONG RANGE B REFINED ATOMS (A**2): 5075 ; 5.659 ;16.400 REMARK 3 LONG RANGE B OTHER ATOMS (A**2): 4748 ; 4.859 ;15.152 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 4Z1D COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 01-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000208438. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAY-13 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL26B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN A200 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 65566 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.650 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 (%) : 99.2 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 34.3100 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL 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: NULL REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, HEPES, MAGNESIUM CHLORIDE, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 70.15000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 25.50650 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 70.15000 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 25.50650 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: 3570 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20730 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -20.0 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 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 B 608 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 669 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 1 REMARK 465 LYS A 2 REMARK 465 THR A 3 REMARK 465 SER A 4 REMARK 465 LYS A 5 REMARK 465 THR A 6 REMARK 465 LYS A 7 REMARK 465 THR A 8 REMARK 465 PRO A 9 REMARK 465 GLY A 210 REMARK 465 GLY A 211 REMARK 465 ALA A 212 REMARK 465 ASN A 213 REMARK 465 GLY A 214 REMARK 465 LYS A 215 REMARK 465 SER A 216 REMARK 465 SER A 217 REMARK 465 GLY A 218 REMARK 465 ASP A 219 REMARK 465 SER A 220 REMARK 465 MET B 1 REMARK 465 LYS B 2 REMARK 465 THR B 3 REMARK 465 SER B 4 REMARK 465 LYS B 5 REMARK 465 THR B 6 REMARK 465 LYS B 7 REMARK 465 THR B 8 REMARK 465 PRO B 9 REMARK 465 GLY B 210 REMARK 465 GLY B 211 REMARK 465 ALA B 212 REMARK 465 ASN B 213 REMARK 465 GLY B 214 REMARK 465 LYS B 215 REMARK 465 SER B 216 REMARK 465 SER B 217 REMARK 465 GLY B 218 REMARK 465 ASP B 219 REMARK 465 SER B 220 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 OE1 GLU B 241 ZN ZN B 301 1.38 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 693 DISTANCE = 6.02 ANGSTROMS REMARK 525 HOH A 694 DISTANCE = 6.30 ANGSTROMS REMARK 525 HOH A 695 DISTANCE = 6.30 ANGSTROMS REMARK 525 HOH A 696 DISTANCE = 6.70 ANGSTROMS REMARK 525 HOH A 697 DISTANCE = 6.84 ANGSTROMS REMARK 525 HOH A 698 DISTANCE = 7.14 ANGSTROMS REMARK 525 HOH A 699 DISTANCE = 7.72 ANGSTROMS REMARK 525 HOH B 692 DISTANCE = 6.00 ANGSTROMS REMARK 525 HOH B 693 DISTANCE = 6.26 ANGSTROMS REMARK 525 HOH B 694 DISTANCE = 6.31 ANGSTROMS REMARK 525 HOH B 695 DISTANCE = 6.87 ANGSTROMS REMARK 525 HOH B 696 DISTANCE = 7.30 ANGSTROMS 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 301 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 CYS A 18 SG REMARK 620 2 HIS A 204 NE2 138.1 REMARK 620 3 GLU A 241 OE1 108.7 100.8 REMARK 620 4 ASP A 252 OD2 110.9 90.6 102.0 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEP A 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue PEP B 300 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN B 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4Z1A RELATED DB: PDB REMARK 900 APO FORM OF THE SAME PROTEIN REMARK 900 RELATED ID: 4Z1B RELATED DB: PDB REMARK 900 MUTANT OF THE SAME PROTEIN REMARK 900 RELATED ID: 4Z1C RELATED DB: PDB REMARK 900 CADMIUN BOUND FORM OF THE SAME PROTEIN DBREF 4Z1D A 1 276 UNP P56060 KDSA_HELPY 1 276 DBREF 4Z1D B 1 276 UNP P56060 KDSA_HELPY 1 276 SEQRES 1 A 276 MET LYS THR SER LYS THR LYS THR PRO LYS SER VAL LEU SEQRES 2 A 276 ILE ALA GLY PRO CYS VAL ILE GLU SER LEU GLU ASN LEU SEQRES 3 A 276 ARG SER ILE ALA THR LYS LEU GLN PRO LEU ALA ASN ASN SEQRES 4 A 276 GLU ARG LEU ASP PHE TYR PHE LYS ALA SER PHE ASP LYS SEQRES 5 A 276 ALA ASN ARG THR SER LEU GLU SER TYR ARG GLY PRO GLY SEQRES 6 A 276 LEU GLU LYS GLY LEU GLU MET LEU GLN THR ILE LYS GLU SEQRES 7 A 276 GLU PHE GLY TYR LYS ILE LEU THR ASP VAL HIS GLU SER SEQRES 8 A 276 TYR GLN ALA SER VAL ALA ALA LYS VAL ALA ASP ILE LEU SEQRES 9 A 276 GLN ILE PRO ALA PHE LEU CYS ARG GLN THR ASP LEU ILE SEQRES 10 A 276 VAL GLU VAL SER GLN THR ASN ALA ILE VAL ASN ILE LYS SEQRES 11 A 276 LYS GLY GLN PHE MET ASN PRO LYS ASP MET GLN TYR SER SEQRES 12 A 276 VAL LEU LYS ALA LEU LYS THR ARG ASP LYS SER ILE GLN SEQRES 13 A 276 SER PRO THR TYR GLU THR ALA LEU LYS ASN GLY VAL TRP SEQRES 14 A 276 LEU CYS GLU ARG GLY SER SER PHE GLY TYR GLY ASN LEU SEQRES 15 A 276 VAL VAL ASP MET ARG SER LEU LYS ILE MET ARG GLU PHE SEQRES 16 A 276 ALA PRO VAL ILE PHE ASP ALA THR HIS SER VAL GLN MET SEQRES 17 A 276 PRO GLY GLY ALA ASN GLY LYS SER SER GLY ASP SER SER SEQRES 18 A 276 PHE ALA PRO ILE LEU ALA ARG ALA ALA ALA ALA VAL GLY SEQRES 19 A 276 ILE ASP GLY LEU PHE ALA GLU THR HIS VAL ASP PRO LYS SEQRES 20 A 276 ASN ALA LEU SER ASP GLY ALA ASN MET LEU LYS PRO ASP SEQRES 21 A 276 GLU LEU GLU GLN LEU VAL THR ASP MET LEU LYS ILE GLN SEQRES 22 A 276 ASN LEU PHE SEQRES 1 B 276 MET LYS THR SER LYS THR LYS THR PRO LYS SER VAL LEU SEQRES 2 B 276 ILE ALA GLY PRO CYS VAL ILE GLU SER LEU GLU ASN LEU SEQRES 3 B 276 ARG SER ILE ALA THR LYS LEU GLN PRO LEU ALA ASN ASN SEQRES 4 B 276 GLU ARG LEU ASP PHE TYR PHE LYS ALA SER PHE ASP LYS SEQRES 5 B 276 ALA ASN ARG THR SER LEU GLU SER TYR ARG GLY PRO GLY SEQRES 6 B 276 LEU GLU LYS GLY LEU GLU MET LEU GLN THR ILE LYS GLU SEQRES 7 B 276 GLU PHE GLY TYR LYS ILE LEU THR ASP VAL HIS GLU SER SEQRES 8 B 276 TYR GLN ALA SER VAL ALA ALA LYS VAL ALA ASP ILE LEU SEQRES 9 B 276 GLN ILE PRO ALA PHE LEU CYS ARG GLN THR ASP LEU ILE SEQRES 10 B 276 VAL GLU VAL SER GLN THR ASN ALA ILE VAL ASN ILE LYS SEQRES 11 B 276 LYS GLY GLN PHE MET ASN PRO LYS ASP MET GLN TYR SER SEQRES 12 B 276 VAL LEU LYS ALA LEU LYS THR ARG ASP LYS SER ILE GLN SEQRES 13 B 276 SER PRO THR TYR GLU THR ALA LEU LYS ASN GLY VAL TRP SEQRES 14 B 276 LEU CYS GLU ARG GLY SER SER PHE GLY TYR GLY ASN LEU SEQRES 15 B 276 VAL VAL ASP MET ARG SER LEU LYS ILE MET ARG GLU PHE SEQRES 16 B 276 ALA PRO VAL ILE PHE ASP ALA THR HIS SER VAL GLN MET SEQRES 17 B 276 PRO GLY GLY ALA ASN GLY LYS SER SER GLY ASP SER SER SEQRES 18 B 276 PHE ALA PRO ILE LEU ALA ARG ALA ALA ALA ALA VAL GLY SEQRES 19 B 276 ILE ASP GLY LEU PHE ALA GLU THR HIS VAL ASP PRO LYS SEQRES 20 B 276 ASN ALA LEU SER ASP GLY ALA ASN MET LEU LYS PRO ASP SEQRES 21 B 276 GLU LEU GLU GLN LEU VAL THR ASP MET LEU LYS ILE GLN SEQRES 22 B 276 ASN LEU PHE HET PEP A 300 10 HET ZN A 301 1 HET PEP B 300 10 HET ZN B 301 1 HETNAM PEP PHOSPHOENOLPYRUVATE HETNAM ZN ZINC ION FORMUL 3 PEP 2(C3 H5 O6 P) FORMUL 4 ZN 2(ZN 2+) FORMUL 7 HOH *595(H2 O) HELIX 1 AA1 SER A 22 LEU A 33 1 12 HELIX 2 AA2 LEU A 33 ASN A 38 1 6 HELIX 3 AA3 GLY A 65 GLY A 81 1 17 HELIX 4 AA4 GLN A 93 ALA A 98 1 6 HELIX 5 AA5 PRO A 107 CYS A 111 5 5 HELIX 6 AA6 GLN A 113 THR A 123 1 11 HELIX 7 AA7 ASN A 136 LYS A 138 5 3 HELIX 8 AA8 ASP A 139 ASP A 152 1 14 HELIX 9 AA9 THR A 159 GLY A 167 1 9 HELIX 10 AB1 MET A 186 GLU A 194 1 9 HELIX 11 AB2 PHE A 222 GLY A 234 1 13 HELIX 12 AB3 ASP A 245 ALA A 249 5 5 HELIX 13 AB4 ASP A 252 MET A 256 5 5 HELIX 14 AB5 LYS A 258 PHE A 276 1 19 HELIX 15 AB6 SER B 22 LEU B 33 1 12 HELIX 16 AB7 LEU B 33 ASN B 38 1 6 HELIX 17 AB8 GLY B 65 GLY B 81 1 17 HELIX 18 AB9 GLU B 90 TYR B 92 5 3 HELIX 19 AC1 GLN B 93 ALA B 98 1 6 HELIX 20 AC2 PRO B 107 CYS B 111 5 5 HELIX 21 AC3 GLN B 113 GLN B 122 1 10 HELIX 22 AC4 ASN B 136 LYS B 138 5 3 HELIX 23 AC5 ASP B 139 ASP B 152 1 14 HELIX 24 AC6 THR B 159 GLY B 167 1 9 HELIX 25 AC7 MET B 186 ARG B 193 1 8 HELIX 26 AC8 PHE B 222 GLY B 234 1 13 HELIX 27 AC9 ASP B 245 ALA B 249 5 5 HELIX 28 AD1 ASP B 252 MET B 256 5 5 HELIX 29 AD2 LYS B 258 LEU B 275 1 18 SHEET 1 AA1 9 SER A 11 GLY A 16 0 SHEET 2 AA1 9 LEU A 42 LYS A 47 1 O TYR A 45 N LEU A 13 SHEET 3 AA1 9 LYS A 83 ASP A 87 1 O LYS A 83 N PHE A 46 SHEET 4 AA1 9 ILE A 103 ILE A 106 1 O GLN A 105 N THR A 86 SHEET 5 AA1 9 ILE A 126 LYS A 130 1 O ILE A 126 N LEU A 104 SHEET 6 AA1 9 VAL A 168 GLU A 172 1 O TRP A 169 N VAL A 127 SHEET 7 AA1 9 VAL A 198 ASP A 201 1 O ASP A 201 N GLU A 172 SHEET 8 AA1 9 GLY A 237 GLU A 241 1 O PHE A 239 N PHE A 200 SHEET 9 AA1 9 SER A 11 GLY A 16 1 N ILE A 14 O LEU A 238 SHEET 1 AA2 2 SER A 175 SER A 176 0 SHEET 2 AA2 2 LEU A 182 VAL A 183 -1 O VAL A 183 N SER A 175 SHEET 1 AA3 9 SER B 11 GLY B 16 0 SHEET 2 AA3 9 LEU B 42 LYS B 47 1 O TYR B 45 N LEU B 13 SHEET 3 AA3 9 LYS B 83 ASP B 87 1 O LYS B 83 N PHE B 46 SHEET 4 AA3 9 ILE B 103 ILE B 106 1 O GLN B 105 N THR B 86 SHEET 5 AA3 9 ILE B 126 LYS B 130 1 O ILE B 126 N LEU B 104 SHEET 6 AA3 9 VAL B 168 GLU B 172 1 O TRP B 169 N VAL B 127 SHEET 7 AA3 9 VAL B 198 ASP B 201 1 O ILE B 199 N LEU B 170 SHEET 8 AA3 9 GLY B 237 GLU B 241 1 O PHE B 239 N PHE B 200 SHEET 9 AA3 9 SER B 11 GLY B 16 1 N ILE B 14 O LEU B 238 SHEET 1 AA4 2 SER B 175 SER B 176 0 SHEET 2 AA4 2 LEU B 182 VAL B 183 -1 O VAL B 183 N SER B 175 LINK SG CYS A 18 ZN ZN A 301 1555 1555 2.31 LINK NE2 HIS A 204 ZN ZN A 301 1555 1555 2.14 LINK OE1 GLU A 241 ZN ZN A 301 1555 1555 1.90 LINK OD2 ASP A 252 ZN ZN A 301 1555 1555 2.05 SITE 1 AC1 14 LYS A 47 SER A 49 LYS A 52 GLN A 105 SITE 2 AC1 14 PRO A 107 ALA A 108 LYS A 130 ARG A 173 SITE 3 AC1 14 HIS A 204 PHE A 239 HOH A 423 HOH A 445 SITE 4 AC1 14 HOH A 512 HOH A 544 SITE 1 AC2 4 CYS A 18 HIS A 204 GLU A 241 ASP A 252 SITE 1 AC3 14 LYS B 47 SER B 49 LYS B 52 GLN B 105 SITE 2 AC3 14 PRO B 107 ALA B 108 LYS B 130 ARG B 173 SITE 3 AC3 14 HIS B 204 PHE B 239 HOH B 405 HOH B 459 SITE 4 AC3 14 HOH B 500 HOH B 545 SITE 1 AC4 5 CYS B 18 THR B 203 HIS B 204 GLU B 241 SITE 2 AC4 5 ASP B 252 CRYST1 140.300 51.013 78.547 90.00 104.37 90.00 C 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 0.007128 0.000000 0.001826 0.00000 SCALE2 0.000000 0.019603 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013143 0.00000