HEADER TRANSFERASE 19-NOV-10 3PNK TITLE CRYSTAL STRUCTURE OF E.COLI DHA KINASE DHAK COMPND MOL_ID: 1; COMPND 2 MOLECULE: PTS-DEPENDENT DIHYDROXYACETONE KINASE, DIHYDROXYACETONE- COMPND 3 BINDING SUBUNIT DHAK; COMPND 4 CHAIN: A, B; COMPND 5 EC: 2.7.-.-; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K-12; SOURCE 5 GENE: B1200, DHAK, JW5187, YCGT; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS STRUCTURAL GENOMICS, MONTREAL-KINGSTON BACTERIAL STRUCTURAL GENOMICS KEYWDS 2 INITIATIVE, BSGI, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR R.SHI,L.MCDONALD,A.MATTE,M.CYGLER,I.EKIEL,MONTREAL-KINGSTON BACTERIAL AUTHOR 2 STRUCTURAL GENOMICS INITIATIVE (BSGI) REVDAT 6 06-SEP-23 3PNK 1 REMARK SEQADV LINK REVDAT 5 08-NOV-17 3PNK 1 REMARK REVDAT 4 13-JUL-11 3PNK 1 VERSN REVDAT 3 16-FEB-11 3PNK 1 JRNL REVDAT 2 19-JAN-11 3PNK 1 JRNL REVDAT 1 12-JAN-11 3PNK 0 JRNL AUTH R.SHI,L.MCDONALD,Q.CUI,A.MATTE,M.CYGLER,I.EKIEL JRNL TITL STRUCTURAL AND MECHANISTIC INSIGHT INTO COVALENT SUBSTRATE JRNL TITL 2 BINDING BY ESCHERICHIA COLI DIHYDROXYACETONE KINASE. JRNL REF PROC.NATL.ACAD.SCI.USA V. 108 1302 2011 JRNL REFN ISSN 0027-8424 JRNL PMID 21209328 JRNL DOI 10.1073/PNAS.1012596108 REMARK 2 REMARK 2 RESOLUTION. 2.21 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 2.21 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 49.83 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 30579 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 : 0.210 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1561 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) : 2.21 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.27 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1742 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 76.45 REMARK 3 BIN R VALUE (WORKING SET) : 0.2190 REMARK 3 BIN FREE R VALUE SET COUNT : 92 REMARK 3 BIN FREE R VALUE : 0.2980 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 5308 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 12 REMARK 3 SOLVENT ATOMS : 165 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 30.66 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.19000 REMARK 3 B22 (A**2) : -0.56000 REMARK 3 B33 (A**2) : 0.75000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.210 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.140 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 11.435 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.957 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 5423 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 7374 ; 1.354 ; 1.966 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 708 ; 6.351 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 230 ;30.590 ;25.043 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 872 ;15.709 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 26 ;20.742 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 852 ; 0.085 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4104 ; 0.004 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 2423 ; 0.204 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 3737 ; 0.301 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 273 ; 0.162 ; 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): 51 ; 0.241 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 1 ; 0.123 ; 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): 3579 ; 0.635 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 5598 ; 1.081 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2066 ; 1.780 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1775 ; 2.839 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 12 A 366 REMARK 3 ORIGIN FOR THE GROUP (A): 14.3756 -0.3438 24.8006 REMARK 3 T TENSOR REMARK 3 T11: -0.0750 T22: -0.0613 REMARK 3 T33: -0.0290 T12: -0.0005 REMARK 3 T13: -0.0121 T23: -0.0089 REMARK 3 L TENSOR REMARK 3 L11: 0.1258 L22: 0.8764 REMARK 3 L33: 0.8209 L12: -0.1024 REMARK 3 L13: 0.1611 L23: -0.1362 REMARK 3 S TENSOR REMARK 3 S11: 0.0142 S12: -0.0174 S13: 0.0593 REMARK 3 S21: 0.0070 S22: -0.0170 S23: -0.0317 REMARK 3 S31: -0.0293 S32: 0.0263 S33: 0.0028 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 12 B 366 REMARK 3 ORIGIN FOR THE GROUP (A): 14.3207 -30.4336 11.7791 REMARK 3 T TENSOR REMARK 3 T11: -0.0692 T22: -0.0580 REMARK 3 T33: -0.0284 T12: -0.0081 REMARK 3 T13: -0.0155 T23: -0.0140 REMARK 3 L TENSOR REMARK 3 L11: 0.0936 L22: 0.7723 REMARK 3 L33: 0.8095 L12: 0.0077 REMARK 3 L13: -0.1677 L23: -0.1570 REMARK 3 S TENSOR REMARK 3 S11: 0.0121 S12: 0.0268 S13: -0.0649 REMARK 3 S21: -0.0146 S22: -0.0073 S23: -0.0295 REMARK 3 S31: 0.0181 S32: 0.0278 S33: -0.0048 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 3PNK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 30-NOV-10. REMARK 100 THE DEPOSITION ID IS D_1000062592. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-DEC-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 31-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK, HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30618 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.210 REMARK 200 RESOLUTION RANGE LOW (A) : 49.830 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.3 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : 0.12200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 9.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.21 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.29 REMARK 200 COMPLETENESS FOR SHELL (%) : 81.1 REMARK 200 DATA REDUNDANCY IN SHELL : 2.70 REMARK 200 R MERGE FOR SHELL (I) : 0.45700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: MOLREP REMARK 200 STARTING MODEL: PDB ENTRY 1OI2 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.62 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.18 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG 8000, 0.1M SODIUM CITRATE PH REMARK 280 5.6, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 295K 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 45.75350 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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYM. 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: 4330 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 24810 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -22.0 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 GLY A 0 REMARK 465 SER A 1 REMARK 465 LYS A 356 REMARK 465 GLY B 0 REMARK 465 SER B 1 REMARK 465 LYS B 356 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 GLU A 175 CG CD OE1 OE2 REMARK 470 ASP A 208 CG OD1 OD2 REMARK 470 GLU A 265 CG CD OE1 OE2 REMARK 470 GLU A 338 CG CD OE1 OE2 REMARK 470 ASP B 208 CG OD1 OD2 REMARK 470 GLU B 265 CG CD OE1 OE2 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 A 220 O HOH A 412 2.14 REMARK 500 O THR B 205 NH1 ARG B 225 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 ASN A 6 -121.51 -104.69 REMARK 500 MET A 68 -131.37 -139.46 REMARK 500 ASP A 133 56.43 -142.81 REMARK 500 TYR A 143 144.01 136.22 REMARK 500 THR A 144 -52.37 146.63 REMARK 500 VAL A 150 -137.52 -129.68 REMARK 500 ALA A 198 47.25 -86.14 REMARK 500 ALA A 199 -57.61 -128.47 REMARK 500 LEU A 323 -125.06 49.68 REMARK 500 ASN B 6 -123.37 -107.35 REMARK 500 ASP B 31 66.41 60.20 REMARK 500 MET B 68 -129.18 -142.08 REMARK 500 ASP B 133 52.23 -141.21 REMARK 500 TYR B 143 -90.44 -172.61 REMARK 500 THR B 144 15.64 122.16 REMARK 500 VAL B 150 -136.88 -125.80 REMARK 500 ALA B 198 44.69 -86.79 REMARK 500 ALA B 199 -52.75 -134.23 REMARK 500 LEU B 323 -123.79 53.42 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 TRP A 354 GLY A 355 -142.69 REMARK 500 TRP B 354 GLY B 355 -140.34 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 GOL A 1228 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL B 1228 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3PNQ RELATED DB: PDB REMARK 900 RELATED ID: 3PNL RELATED DB: PDB REMARK 900 RELATED ID: 3PNM RELATED DB: PDB REMARK 900 RELATED ID: 3PNO RELATED DB: PDB DBREF 3PNK A 2 356 UNP P76015 DHAK_ECOLI 2 356 DBREF 3PNK B 2 356 UNP P76015 DHAK_ECOLI 2 356 SEQADV 3PNK GLY A 0 UNP P76015 EXPRESSION TAG SEQADV 3PNK SER A 1 UNP P76015 EXPRESSION TAG SEQADV 3PNK GLY B 0 UNP P76015 EXPRESSION TAG SEQADV 3PNK SER B 1 UNP P76015 EXPRESSION TAG SEQRES 1 A 357 GLY SER LYS LYS LEU ILE ASN ASP VAL GLN ASP VAL LEU SEQRES 2 A 357 ASP GLU GLN LEU ALA GLY LEU ALA LYS ALA HIS PRO SER SEQRES 3 A 357 LEU THR LEU HIS GLN ASP PRO VAL TYR VAL THR ARG ALA SEQRES 4 A 357 ASP ALA PRO VAL ALA GLY LYS VAL ALA LEU LEU SER GLY SEQRES 5 A 357 GLY GLY SER GLY HIS GLU PRO MET HIS CYS GLY TYR ILE SEQRES 6 A 357 GLY GLN GLY MET LEU SER GLY ALA CYS PRO GLY GLU ILE SEQRES 7 A 357 PHE THR SER PRO THR PRO ASP LYS ILE PHE GLU CYS ALA SEQRES 8 A 357 MET GLN VAL ASP GLY GLY GLU GLY VAL LEU LEU ILE ILE SEQRES 9 A 357 LYS ASN TYR THR GLY ASP ILE LEU ASN PHE GLU THR ALA SEQRES 10 A 357 THR GLU LEU LEU HIS ASP SER GLY VAL LYS VAL THR THR SEQRES 11 A 357 VAL VAL ILE ASP ASP ASP VAL ALA VAL LYS ASP SER LEU SEQRES 12 A 357 TYR THR ALA GLY ARG ARG GLY VAL ALA ASN THR VAL LEU SEQRES 13 A 357 ILE GLU LYS LEU VAL GLY ALA ALA ALA GLU ARG GLY ASP SEQRES 14 A 357 SER LEU ASP ALA CYS ALA GLU LEU GLY ARG LYS LEU ASN SEQRES 15 A 357 ASN GLN GLY HIS SER ILE GLY ILE ALA LEU GLY ALA CYS SEQRES 16 A 357 THR VAL PRO ALA ALA GLY LYS PRO SER PHE THR LEU ALA SEQRES 17 A 357 ASP ASN GLU MET GLU PHE GLY VAL GLY ILE HIS GLY GLU SEQRES 18 A 357 PRO GLY ILE ASP ARG ARG PRO PHE SER SER LEU ASP GLN SEQRES 19 A 357 THR VAL ASP GLU MET PHE ASP THR LEU LEU VAL ASN GLY SEQRES 20 A 357 SER TYR HIS ARG THR LEU ARG PHE TRP ASP TYR GLN GLN SEQRES 21 A 357 GLY SER TRP GLN GLU GLU GLN GLN THR LYS GLN PRO LEU SEQRES 22 A 357 GLN SER GLY ASP ARG VAL ILE ALA LEU VAL ASN ASN LEU SEQRES 23 A 357 GLY ALA THR PRO LEU SER GLU LEU TYR GLY VAL TYR ASN SEQRES 24 A 357 ARG LEU THR THR ARG CYS GLN GLN ALA GLY LEU THR ILE SEQRES 25 A 357 GLU ARG ASN LEU ILE GLY ALA TYR CYS THR SER LEU ASP SEQRES 26 A 357 MET THR GLY PHE SER ILE THR LEU LEU LYS VAL ASP ASP SEQRES 27 A 357 GLU THR LEU ALA LEU TRP ASP ALA PRO VAL HIS THR PRO SEQRES 28 A 357 ALA LEU ASN TRP GLY LYS SEQRES 1 B 357 GLY SER LYS LYS LEU ILE ASN ASP VAL GLN ASP VAL LEU SEQRES 2 B 357 ASP GLU GLN LEU ALA GLY LEU ALA LYS ALA HIS PRO SER SEQRES 3 B 357 LEU THR LEU HIS GLN ASP PRO VAL TYR VAL THR ARG ALA SEQRES 4 B 357 ASP ALA PRO VAL ALA GLY LYS VAL ALA LEU LEU SER GLY SEQRES 5 B 357 GLY GLY SER GLY HIS GLU PRO MET HIS CYS GLY TYR ILE SEQRES 6 B 357 GLY GLN GLY MET LEU SER GLY ALA CYS PRO GLY GLU ILE SEQRES 7 B 357 PHE THR SER PRO THR PRO ASP LYS ILE PHE GLU CYS ALA SEQRES 8 B 357 MET GLN VAL ASP GLY GLY GLU GLY VAL LEU LEU ILE ILE SEQRES 9 B 357 LYS ASN TYR THR GLY ASP ILE LEU ASN PHE GLU THR ALA SEQRES 10 B 357 THR GLU LEU LEU HIS ASP SER GLY VAL LYS VAL THR THR SEQRES 11 B 357 VAL VAL ILE ASP ASP ASP VAL ALA VAL LYS ASP SER LEU SEQRES 12 B 357 TYR THR ALA GLY ARG ARG GLY VAL ALA ASN THR VAL LEU SEQRES 13 B 357 ILE GLU LYS LEU VAL GLY ALA ALA ALA GLU ARG GLY ASP SEQRES 14 B 357 SER LEU ASP ALA CYS ALA GLU LEU GLY ARG LYS LEU ASN SEQRES 15 B 357 ASN GLN GLY HIS SER ILE GLY ILE ALA LEU GLY ALA CYS SEQRES 16 B 357 THR VAL PRO ALA ALA GLY LYS PRO SER PHE THR LEU ALA SEQRES 17 B 357 ASP ASN GLU MET GLU PHE GLY VAL GLY ILE HIS GLY GLU SEQRES 18 B 357 PRO GLY ILE ASP ARG ARG PRO PHE SER SER LEU ASP GLN SEQRES 19 B 357 THR VAL ASP GLU MET PHE ASP THR LEU LEU VAL ASN GLY SEQRES 20 B 357 SER TYR HIS ARG THR LEU ARG PHE TRP ASP TYR GLN GLN SEQRES 21 B 357 GLY SER TRP GLN GLU GLU GLN GLN THR LYS GLN PRO LEU SEQRES 22 B 357 GLN SER GLY ASP ARG VAL ILE ALA LEU VAL ASN ASN LEU SEQRES 23 B 357 GLY ALA THR PRO LEU SER GLU LEU TYR GLY VAL TYR ASN SEQRES 24 B 357 ARG LEU THR THR ARG CYS GLN GLN ALA GLY LEU THR ILE SEQRES 25 B 357 GLU ARG ASN LEU ILE GLY ALA TYR CYS THR SER LEU ASP SEQRES 26 B 357 MET THR GLY PHE SER ILE THR LEU LEU LYS VAL ASP ASP SEQRES 27 B 357 GLU THR LEU ALA LEU TRP ASP ALA PRO VAL HIS THR PRO SEQRES 28 B 357 ALA LEU ASN TRP GLY LYS HET GOL A1228 6 HET GOL B1228 6 HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 GOL 2(C3 H8 O3) FORMUL 5 HOH *165(H2 O) HELIX 1 1 ASP A 7 GLN A 9 5 3 HELIX 2 2 ASP A 10 HIS A 23 1 14 HELIX 3 3 HIS A 60 ILE A 64 5 5 HELIX 4 4 THR A 82 ASP A 94 1 13 HELIX 5 5 TYR A 106 SER A 123 1 18 HELIX 6 6 ALA A 151 GLY A 167 1 17 HELIX 7 7 SER A 169 ASN A 182 1 14 HELIX 8 8 SER A 230 ASN A 245 1 16 HELIX 9 9 PRO A 289 ALA A 307 1 19 HELIX 10 10 ASP A 336 ALA A 345 1 10 HELIX 11 11 ASP B 7 GLN B 9 5 3 HELIX 12 12 ASP B 10 HIS B 23 1 14 HELIX 13 13 HIS B 60 ILE B 64 5 5 HELIX 14 14 THR B 82 ASP B 94 1 13 HELIX 15 15 TYR B 106 SER B 123 1 18 HELIX 16 16 ALA B 151 GLY B 167 1 17 HELIX 17 17 SER B 169 ASN B 182 1 14 HELIX 18 18 SER B 230 ASN B 245 1 16 HELIX 19 19 PRO B 289 GLY B 308 1 20 HELIX 20 20 ASP B 336 ALA B 345 1 10 SHEET 1 A 6 LEU A 26 HIS A 29 0 SHEET 2 A 6 TYR A 34 ARG A 37 -1 O TYR A 34 N HIS A 29 SHEET 3 A 6 GLY A 71 ILE A 77 -1 O ALA A 72 N VAL A 35 SHEET 4 A 6 ALA A 47 SER A 54 1 N GLY A 52 O GLY A 75 SHEET 5 A 6 VAL A 99 LYS A 104 1 O LEU A 100 N ALA A 47 SHEET 6 A 6 VAL A 127 ILE A 132 1 O VAL A 130 N ILE A 103 SHEET 1 B 6 ASP A 224 PRO A 227 0 SHEET 2 B 6 GLU A 210 PHE A 213 -1 N MET A 211 O ARG A 226 SHEET 3 B 6 GLY A 184 GLY A 192 -1 N ALA A 190 O GLU A 212 SHEET 4 B 6 THR A 326 VAL A 335 -1 O THR A 326 N LEU A 191 SHEET 5 B 6 ARG A 277 ASN A 284 -1 N ARG A 277 O VAL A 335 SHEET 6 B 6 THR A 310 GLY A 317 1 O GLU A 312 N VAL A 278 SHEET 1 C 2 TYR A 248 ASP A 256 0 SHEET 2 C 2 SER A 261 LYS A 269 -1 O GLN A 263 N PHE A 254 SHEET 1 D 2 VAL A 347 HIS A 348 0 SHEET 2 D 2 ASN A 353 TRP A 354 -1 O TRP A 354 N VAL A 347 SHEET 1 E 6 LEU B 26 HIS B 29 0 SHEET 2 E 6 TYR B 34 ARG B 37 -1 O TYR B 34 N HIS B 29 SHEET 3 E 6 GLY B 71 ILE B 77 -1 O ALA B 72 N VAL B 35 SHEET 4 E 6 ALA B 47 SER B 54 1 N GLY B 52 O GLY B 75 SHEET 5 E 6 VAL B 99 LYS B 104 1 O LEU B 100 N ALA B 47 SHEET 6 E 6 VAL B 127 ILE B 132 1 O VAL B 130 N ILE B 103 SHEET 1 F 6 ASP B 224 PRO B 227 0 SHEET 2 F 6 GLU B 210 PHE B 213 -1 N PHE B 213 O ASP B 224 SHEET 3 F 6 GLY B 184 GLY B 192 -1 N ALA B 190 O GLU B 212 SHEET 4 F 6 THR B 326 VAL B 335 -1 O THR B 326 N LEU B 191 SHEET 5 F 6 ARG B 277 ASN B 284 -1 N ARG B 277 O VAL B 335 SHEET 6 F 6 THR B 310 GLY B 317 1 O THR B 310 N VAL B 278 SHEET 1 G 2 TYR B 248 ASP B 256 0 SHEET 2 G 2 SER B 261 LYS B 269 -1 O LYS B 269 N TYR B 248 SHEET 1 H 2 VAL B 347 HIS B 348 0 SHEET 2 H 2 ASN B 353 TRP B 354 -1 O TRP B 354 N VAL B 347 LINK NE2 HIS A 218 C2 GOL A1228 1555 1555 1.82 LINK NE2 HIS B 218 C2 GOL B1228 1555 1555 1.32 CISPEP 1 ASP A 31 PRO A 32 0 -0.12 CISPEP 2 ALA A 40 PRO A 41 0 -5.76 CISPEP 3 GLU A 57 PRO A 58 0 7.09 CISPEP 4 MET A 59 HIS A 60 0 1.87 CISPEP 5 TYR A 143 THR A 144 0 -26.43 CISPEP 6 ASP B 31 PRO B 32 0 1.56 CISPEP 7 ALA B 40 PRO B 41 0 -0.99 CISPEP 8 GLU B 57 PRO B 58 0 2.78 CISPEP 9 MET B 59 HIS B 60 0 3.60 SITE 1 AC1 9 GLY A 52 GLY A 53 HIS A 56 PHE A 78 SITE 2 AC1 9 SER A 80 LYS A 104 ASP A 109 HIS A 218 SITE 3 AC1 9 HOH A 420 SITE 1 AC2 8 GLY B 52 GLY B 53 HIS B 56 PHE B 78 SITE 2 AC2 8 LYS B 104 ASP B 109 HIS B 218 HOH B 419 CRYST1 49.833 91.507 73.232 90.00 89.96 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 0.020067 0.000000 -0.000014 0.00000 SCALE2 0.000000 0.010928 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013655 0.00000