HEADER ISOMERASE/HYDROLASE/RNA 12-APR-18 6D1V TITLE CRYSTAL STRUCTURE OF E. COLI RPPH-DAPF COMPLEX, MONOMER BOUND TO RNA COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIAMINOPIMELATE EPIMERASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MOL_ID: 2; COMPND 6 MOLECULE: RNA PYROPHOSPHOHYDROLASE; COMPND 7 CHAIN: B; COMPND 8 SYNONYM: (DI)NUCLEOSIDE POLYPHOSPHATE HYDROLASE,AP5A PYROPHOSPHATASE; COMPND 9 EC: 3.6.1.-; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: RNA (5'-D(*(APC))-R(P*GP*U)-3'); COMPND 13 CHAIN: C; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: DAPF; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 10 ORGANISM_TAXID: 83333; SOURCE 11 STRAIN: K12; SOURCE 12 GENE: RPPH, NUDH, YGDP, B2830, JW2798; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 15 MOL_ID: 3; SOURCE 16 SYNTHETIC: YES; SOURCE 17 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 18 ORGANISM_TAXID: 562 KEYWDS RNA DECAY, RPPH, DAPF, ISOMERASE-HYDROLASE COMPLEX, ISOMERASE- KEYWDS 2 HYDROLASE-RNA COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.GAO,A.SERGANOV REVDAT 4 13-MAR-24 6D1V 1 LINK REVDAT 3 04-DEC-19 6D1V 1 REMARK REVDAT 2 08-AUG-18 6D1V 1 COMPND SOURCE JRNL DBREF REVDAT 2 2 1 SEQADV REVDAT 1 23-MAY-18 6D1V 0 JRNL AUTH A.GAO,N.VASILYEV,D.J.LUCIANO,R.LEVENSON-PALMER,J.RICHARDS, JRNL AUTH 2 W.M.MARSIGLIA,N.J.TRAASETH,J.G.BELASCO,A.SERGANOV JRNL TITL STRUCTURAL AND KINETIC INSIGHTS INTO STIMULATION OF JRNL TITL 2 RPPH-DEPENDENT RNA DEGRADATION BY THE METABOLIC ENZYME DAPF. JRNL REF NUCLEIC ACIDS RES. V. 46 6841 2018 JRNL REFN ESSN 1362-4962 JRNL PMID 29733359 JRNL DOI 10.1093/NAR/GKY327 REMARK 2 REMARK 2 RESOLUTION. 1.81 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.81 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 61.60 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 70302 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.199 REMARK 3 R VALUE (WORKING SET) : 0.199 REMARK 3 FREE R VALUE : 0.220 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.840 REMARK 3 FREE R VALUE TEST SET COUNT : 2000 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 61.6371 - 4.3627 0.94 5025 148 0.1661 0.1710 REMARK 3 2 4.3627 - 3.4629 0.95 4865 142 0.1676 0.1809 REMARK 3 3 3.4629 - 3.0252 0.96 4872 142 0.1995 0.2314 REMARK 3 4 3.0252 - 2.7486 0.98 4915 144 0.2097 0.2164 REMARK 3 5 2.7486 - 2.5516 0.97 4877 143 0.2215 0.2649 REMARK 3 6 2.5516 - 2.4011 0.99 4989 146 0.2167 0.2689 REMARK 3 7 2.4011 - 2.2809 0.99 4926 145 0.2269 0.2934 REMARK 3 8 2.2809 - 2.1816 0.99 4963 145 0.2228 0.2498 REMARK 3 9 2.1816 - 2.0976 0.99 4945 145 0.2297 0.2674 REMARK 3 10 2.0976 - 2.0252 0.99 4942 144 0.2496 0.2554 REMARK 3 11 2.0252 - 1.9619 0.99 4936 144 0.2565 0.2767 REMARK 3 12 1.9619 - 1.9058 0.99 4931 146 0.2815 0.3315 REMARK 3 13 1.9058 - 1.8556 0.99 4977 145 0.3150 0.3624 REMARK 3 14 1.8556 - 1.8104 0.83 4139 121 0.3399 0.3693 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.260 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.100 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.008 3630 REMARK 3 ANGLE : 1.036 4918 REMARK 3 CHIRALITY : 0.058 520 REMARK 3 PLANARITY : 0.006 633 REMARK 3 DIHEDRAL : 5.838 2970 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6D1V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-APR-18. REMARK 100 THE DEPOSITION ID IS D_1000233868. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-MAR-16 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 : 24-ID-C REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97910 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 70344 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.810 REMARK 200 RESOLUTION RANGE LOW (A) : 123.200 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.03700 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 12.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.81 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.98900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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 (%): 68.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.92 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (V/V) PEG400 AND 0.1 M CHES, PH REMARK 280 9.2, VAPOR DIFFUSION, TEMPERATURE 292K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 25.60350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 25.60350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 80.32200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 95.99300 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 80.32200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 95.99300 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 25.60350 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 80.32200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 95.99300 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 25.60350 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 80.32200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 95.99300 REMARK 290 SMTRY3 8 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 CL CL B 207 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 ALA B 159 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 36 CG CD NE CZ NH1 NH2 REMARK 470 TYR A 268 CG CD1 CD2 CE1 CE2 CZ OH REMARK 470 U C 3 C5' C4' O4' C3' O3' C2' O2' REMARK 470 U C 3 C1' N1 C2 O2 N3 C4 O4 REMARK 470 U C 3 C5 C6 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 ALA A 144 -125.59 54.39 REMARK 500 GLU A 145 37.20 -88.73 REMARK 500 ARG A 188 -179.22 61.02 REMARK 500 ARG A 199 -19.15 -47.23 REMARK 500 ALA A 216 72.87 -157.55 REMARK 500 MET B 113 30.63 -96.27 REMARK 500 GLN B 114 35.77 -144.34 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 GOL A 803 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 B 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN B 37 O REMARK 620 2 GLU B 57 OE2 93.0 REMARK 620 3 GLU B 120 OE1 171.7 86.1 REMARK 620 4 HOH B 344 O 88.4 92.3 83.4 REMARK 620 5 APC C 1 O3G 85.6 178.5 95.4 88.2 REMARK 620 6 APC C 1 O2B 96.0 88.2 92.2 175.5 91.5 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 201 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 53 OE2 REMARK 620 2 HOH B 314 O 83.4 REMARK 620 3 HOH B 327 O 91.6 97.1 REMARK 620 4 HOH B 369 O 93.7 174.9 78.8 REMARK 620 5 APC C 1 O1B 94.2 87.5 173.0 96.9 REMARK 620 6 HOH C 102 O 172.8 90.0 86.4 92.7 88.3 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 202 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 53 OE1 REMARK 620 2 GLU B 56 OE1 87.1 REMARK 620 3 GLU B 57 OE2 88.6 102.0 REMARK 620 4 GLU B 120 OE2 169.5 84.6 86.8 REMARK 620 5 HOH B 369 O 92.2 82.5 175.4 93.1 REMARK 620 6 APC C 1 O2B 95.3 174.5 83.0 93.5 92.4 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 GOL A 801 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 802 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 803 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL A 804 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 805 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 806 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 807 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 207 DBREF 6D1V A 1 274 UNP P0A6K1 DAPF_ECOLI 1 274 DBREF 6D1V B 1 159 UNP P0A776 RPPH_ECOLI 1 159 DBREF 6D1V C 1 3 PDB 6D1V 6D1V 1 3 SEQADV 6D1V SER A 0 UNP P0A6K1 EXPRESSION TAG SEQADV 6D1V SER B 0 UNP P0A776 EXPRESSION TAG SEQADV 6D1V ALA B 159 UNP P0A776 GLN 159 CONFLICT SEQRES 1 A 275 SER MET GLN PHE SER LYS MET HIS GLY LEU GLY ASN ASP SEQRES 2 A 275 PHE MET VAL VAL ASP ALA VAL THR GLN ASN VAL PHE PHE SEQRES 3 A 275 SER PRO GLU LEU ILE ARG ARG LEU ALA ASP ARG HIS LEU SEQRES 4 A 275 GLY VAL GLY PHE ASP GLN LEU LEU VAL VAL GLU PRO PRO SEQRES 5 A 275 TYR ASP PRO GLU LEU ASP PHE HIS TYR ARG ILE PHE ASN SEQRES 6 A 275 ALA ASP GLY SER GLU VAL ALA GLN CYS GLY ASN GLY ALA SEQRES 7 A 275 ARG CYS PHE ALA ARG PHE VAL ARG LEU LYS GLY LEU THR SEQRES 8 A 275 ASN LYS ARG ASP ILE ARG VAL SER THR ALA ASN GLY ARG SEQRES 9 A 275 MET VAL LEU THR VAL THR ASP ASP ASP LEU VAL ARG VAL SEQRES 10 A 275 ASN MET GLY GLU PRO ASN PHE GLU PRO SER ALA VAL PRO SEQRES 11 A 275 PHE ARG ALA ASN LYS ALA GLU LYS THR TYR ILE MET ARG SEQRES 12 A 275 ALA ALA GLU GLN THR ILE LEU CYS GLY VAL VAL SER MET SEQRES 13 A 275 GLY ASN PRO HIS CYS VAL ILE GLN VAL ASP ASP VAL ASP SEQRES 14 A 275 THR ALA ALA VAL GLU THR LEU GLY PRO VAL LEU GLU SER SEQRES 15 A 275 HIS GLU ARG PHE PRO GLU ARG ALA ASN ILE GLY PHE MET SEQRES 16 A 275 GLN VAL VAL LYS ARG GLU HIS ILE ARG LEU ARG VAL TYR SEQRES 17 A 275 GLU ARG GLY ALA GLY GLU THR GLN ALA CYS GLY SER GLY SEQRES 18 A 275 ALA CYS ALA ALA VAL ALA VAL GLY ILE GLN GLN GLY LEU SEQRES 19 A 275 LEU ALA GLU GLU VAL ARG VAL GLU LEU PRO GLY GLY ARG SEQRES 20 A 275 LEU ASP ILE ALA TRP LYS GLY PRO GLY HIS PRO LEU TYR SEQRES 21 A 275 MET THR GLY PRO ALA VAL HIS VAL TYR ASP GLY PHE ILE SEQRES 22 A 275 HIS LEU SEQRES 1 B 160 SER MET ILE ASP ASP ASP GLY TYR ARG PRO ASN VAL GLY SEQRES 2 B 160 ILE VAL ILE CYS ASN ARG GLN GLY GLN VAL MET TRP ALA SEQRES 3 B 160 ARG ARG PHE GLY GLN HIS SER TRP GLN PHE PRO GLN GLY SEQRES 4 B 160 GLY ILE ASN PRO GLY GLU SER ALA GLU GLN ALA MET TYR SEQRES 5 B 160 ARG GLU LEU PHE GLU GLU VAL GLY LEU SER ARG LYS ASP SEQRES 6 B 160 VAL ARG ILE LEU ALA SER THR ARG ASN TRP LEU ARG TYR SEQRES 7 B 160 LYS LEU PRO LYS ARG LEU VAL ARG TRP ASP THR LYS PRO SEQRES 8 B 160 VAL CYS ILE GLY GLN LYS GLN LYS TRP PHE LEU LEU GLN SEQRES 9 B 160 LEU VAL SER GLY ASP ALA GLU ILE ASN MET GLN THR SER SEQRES 10 B 160 SER THR PRO GLU PHE ASP GLY TRP ARG TRP VAL SER TYR SEQRES 11 B 160 TRP TYR PRO VAL ARG GLN VAL VAL SER PHE LYS ARG ASP SEQRES 12 B 160 VAL TYR ARG ARG VAL MET LYS GLU PHE ALA SER VAL VAL SEQRES 13 B 160 MET SER LEU ALA SEQRES 1 C 3 APC G U HET APC C 1 31 HET GOL A 801 6 HET GOL A 802 6 HET GOL A 803 5 HET GOL A 804 6 HET CL A 805 1 HET CL A 806 1 HET CL A 807 1 HET MG B 201 1 HET MG B 202 1 HET MG B 203 1 HET GOL B 204 6 HET GOL B 205 6 HET GOL B 206 6 HET CL B 207 1 HET CL B 208 1 HETNAM APC DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER HETNAM GOL GLYCEROL HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION HETSYN APC ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 APC C11 H18 N5 O12 P3 FORMUL 4 GOL 7(C3 H8 O3) FORMUL 8 CL 5(CL 1-) FORMUL 11 MG 3(MG 2+) FORMUL 19 HOH *288(H2 O) HELIX 1 AA1 SER A 26 ASP A 35 1 10 HELIX 2 AA2 GLY A 76 LYS A 87 1 12 HELIX 3 AA3 GLU A 124 VAL A 128 5 5 HELIX 4 AA4 THR A 174 SER A 181 1 8 HELIX 5 AA5 CYS A 217 GLN A 231 1 15 HELIX 6 AA6 SER B 45 GLY B 59 1 15 HELIX 7 AA7 SER B 61 LYS B 63 5 3 HELIX 8 AA8 PRO B 80 VAL B 84 5 5 HELIX 9 AA9 GLY B 107 ILE B 111 5 5 HELIX 10 AB1 TRP B 130 VAL B 136 1 7 HELIX 11 AB2 VAL B 137 PHE B 139 5 3 HELIX 12 AB3 LYS B 140 SER B 157 1 18 SHEET 1 AA110 GLU A 69 VAL A 70 0 SHEET 2 AA110 PHE A 58 PHE A 63 -1 N ILE A 62 O VAL A 70 SHEET 3 AA110 ASP A 94 THR A 99 1 O SER A 98 N TYR A 60 SHEET 4 AA110 GLY A 102 VAL A 108 -1 O LEU A 106 N ILE A 95 SHEET 5 AA110 VAL A 114 ASN A 117 -1 O ARG A 115 N THR A 107 SHEET 6 AA110 TYR A 259 GLY A 262 -1 O GLY A 262 N VAL A 114 SHEET 7 AA110 GLY A 245 ALA A 250 -1 N ALA A 250 O TYR A 259 SHEET 8 AA110 GLU A 237 LEU A 242 -1 N LEU A 242 O GLY A 245 SHEET 9 AA110 HIS A 201 GLU A 208 1 N ILE A 202 O ARG A 239 SHEET 10 AA110 GLY A 212 GLU A 213 -1 O GLY A 212 N GLU A 208 SHEET 1 AA216 TYR A 139 ALA A 143 0 SHEET 2 AA216 GLN A 146 SER A 154 -1 O ILE A 148 N MET A 141 SHEET 3 AA216 PRO A 158 GLN A 163 -1 O VAL A 161 N GLY A 151 SHEET 4 AA216 ASN A 190 LYS A 198 1 O ASN A 190 N CYS A 160 SHEET 5 AA216 HIS A 201 GLU A 208 -1 O HIS A 201 N LYS A 198 SHEET 6 AA216 GLU A 237 LEU A 242 1 O ARG A 239 N ILE A 202 SHEET 7 AA216 GLY A 245 ALA A 250 -1 O GLY A 245 N LEU A 242 SHEET 8 AA216 TYR A 259 GLY A 262 -1 O TYR A 259 N ALA A 250 SHEET 9 AA216 VAL A 114 ASN A 117 -1 N VAL A 114 O GLY A 262 SHEET 10 AA216 GLY A 102 VAL A 108 -1 N THR A 107 O ARG A 115 SHEET 11 AA216 ASP A 94 THR A 99 -1 N ILE A 95 O LEU A 106 SHEET 12 AA216 PHE A 58 PHE A 63 1 N TYR A 60 O SER A 98 SHEET 13 AA216 GLN A 44 GLU A 49 -1 N GLU A 49 O HIS A 59 SHEET 14 AA216 ASN A 11 ASP A 17 1 N MET A 14 O LEU A 46 SHEET 15 AA216 MET A 1 GLY A 8 -1 N SER A 4 O VAL A 15 SHEET 16 AA216 VAL A 265 ILE A 272 -1 O VAL A 265 N HIS A 7 SHEET 1 AA3 4 GLN B 37 GLY B 39 0 SHEET 2 AA3 4 TYR B 7 CYS B 16 -1 N VAL B 11 O GLY B 38 SHEET 3 AA3 4 GLY B 94 LEU B 104 1 O LEU B 102 N CYS B 16 SHEET 4 AA3 4 VAL B 65 SER B 70 -1 N ALA B 69 O LEU B 101 SHEET 1 AA4 4 GLN B 37 GLY B 39 0 SHEET 2 AA4 4 TYR B 7 CYS B 16 -1 N VAL B 11 O GLY B 38 SHEET 3 AA4 4 GLY B 94 LEU B 104 1 O LEU B 102 N CYS B 16 SHEET 4 AA4 4 LEU B 75 LYS B 78 -1 N LEU B 75 O GLN B 97 SHEET 1 AA5 3 TRP B 33 GLN B 34 0 SHEET 2 AA5 3 VAL B 22 ARG B 27 -1 N ALA B 25 O GLN B 34 SHEET 3 AA5 3 PHE B 121 VAL B 127 -1 O GLY B 123 N ARG B 26 LINK O3' APC C 1 P G C 2 1555 1555 1.61 LINK O GLN B 37 MG MG B 203 1555 1555 1.97 LINK OE2 GLU B 53 MG MG B 201 1555 1555 1.99 LINK OE1 GLU B 53 MG MG B 202 1555 1555 2.01 LINK OE1 GLU B 56 MG MG B 202 1555 1555 2.12 LINK OE2 GLU B 57 MG MG B 202 1555 1555 2.18 LINK OE2 GLU B 57 MG MG B 203 1555 1555 2.01 LINK OE2 GLU B 120 MG MG B 202 1555 1555 2.01 LINK OE1 GLU B 120 MG MG B 203 1555 1555 2.04 LINK MG MG B 201 O HOH B 314 1555 1555 2.10 LINK MG MG B 201 O HOH B 327 1555 1555 2.26 LINK MG MG B 201 O HOH B 369 1555 1555 2.08 LINK MG MG B 201 O1B APC C 1 1555 1555 2.03 LINK MG MG B 201 O HOH C 102 1555 1555 2.24 LINK MG MG B 202 O HOH B 369 1555 1555 2.20 LINK MG MG B 202 O2B APC C 1 1555 1555 2.07 LINK MG MG B 203 O HOH B 344 1555 1555 2.15 LINK MG MG B 203 O3G APC C 1 1555 1555 1.92 LINK MG MG B 203 O2B APC C 1 1555 1555 2.03 CISPEP 1 VAL A 128 PRO A 129 0 -0.96 CISPEP 2 LYS B 89 PRO B 90 0 -3.68 SITE 1 AC1 7 LEU A 38 TYR A 52 HIS A 59 THR A 99 SITE 2 AC1 7 HOH A 903 HOH A 907 HOH A 938 SITE 1 AC2 6 GLN A 44 ASN A 64 HOH A 922 HOH A 953 SITE 2 AC2 6 PRO B 80 ARG B 82 SITE 1 AC3 5 ARG A 103 MET A 104 VAL A 105 ASN A 117 SITE 2 AC3 5 HOH A 932 SITE 1 AC4 4 HIS A 266 GLN B 114 ASP B 122 HOH B 350 SITE 1 AC5 4 GLY A 76 ARG A 78 CYS A 79 HOH A 982 SITE 1 AC6 3 MET A 141 ARG A 142 ARG A 184 SITE 1 AC7 3 ASN A 157 ARG A 209 LYS B 81 SITE 1 AC8 7 GLU B 53 MG B 202 HOH B 314 HOH B 327 SITE 2 AC8 7 HOH B 369 APC C 1 HOH C 102 SITE 1 AC9 8 GLU B 53 GLU B 56 GLU B 57 GLU B 120 SITE 2 AC9 8 MG B 201 MG B 203 HOH B 369 APC C 1 SITE 1 AD1 6 GLN B 37 GLU B 57 GLU B 120 MG B 202 SITE 2 AD1 6 HOH B 344 APC C 1 SITE 1 AD2 3 ALA B 46 GLU B 47 PHE B 100 SITE 1 AD3 5 ASN A 22 ASP B 142 ARG B 145 HOH B 312 SITE 2 AD3 5 HOH B 352 SITE 1 AD4 5 ILE B 111 ASN B 112 MET B 113 GLN B 114 SITE 2 AD4 5 TRP B 124 SITE 1 AD5 3 SER B 61 ARG B 62 HOH B 427 CRYST1 160.644 191.986 51.207 90.00 90.00 90.00 C 2 2 21 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 0.006225 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005209 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019529 0.00000