HEADER RNA BINDING PROTEIN/ISOMERASE 21-DEC-19 6VCL TITLE CRYSTAL STRUCTURE OF E.COLI RPPH-DAPF IN COMPLEX WITH PPPGPP, MG2+ AND TITLE 2 F- COMPND MOL_ID: 1; COMPND 2 MOLECULE: DIAMINOPIMELATE EPIMERASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: DAP EPIMERASE,PLP-INDEPENDENT AMINO ACID RACEMASE; COMPND 5 EC: 5.1.1.7; COMPND 6 ENGINEERED: YES; COMPND 7 MUTATION: YES; COMPND 8 MOL_ID: 2; COMPND 9 MOLECULE: RNA PYROPHOSPHOHYDROLASE; COMPND 10 CHAIN: B; COMPND 11 SYNONYM: (DI)NUCLEOSIDE POLYPHOSPHATE HYDROLASE,AP5A PYROPHOSPHATASE; COMPND 12 EC: 3.6.1.-; COMPND 13 ENGINEERED: YES; COMPND 14 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12); SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: DAPF, B3809, JW5592; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12); SOURCE 10 ORGANISM_TAXID: 83333; SOURCE 11 STRAIN: K12; SOURCE 12 GENE: RPPH, NUDH, YGDP, B2830, JW2798; SOURCE 13 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 14 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS RNA DEGRADATION, RNA BINDING PROTEIN, RNA BINDING PROTEIN-ISOMERASE KEYWDS 2 COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR A.GAO,N.VASILYEV,A.KAUSHIK,W.DUAN,A.SERGANOV REVDAT 3 11-OCT-23 6VCL 1 LINK REVDAT 2 22-APR-20 6VCL 1 JRNL REVDAT 1 05-FEB-20 6VCL 0 JRNL AUTH A.GAO,N.VASILYEV,A.KAUSHIK,W.DUAN,A.SERGANOV JRNL TITL PRINCIPLES OF RNA AND NUCLEOTIDE DISCRIMINATION BY THE RNA JRNL TITL 2 PROCESSING ENZYME RPPH. JRNL REF NUCLEIC ACIDS RES. V. 48 3776 2020 JRNL REFN ESSN 1362-4962 JRNL PMID 31960065 JRNL DOI 10.1093/NAR/GKAA024 REMARK 2 REMARK 2 RESOLUTION. 2.06 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.16_3546 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) : 2.06 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 48676 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.193 REMARK 3 R VALUE (WORKING SET) : 0.191 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.110 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 30.2100 - 4.9600 0.99 3594 154 0.1730 0.2028 REMARK 3 2 4.9600 - 3.9400 0.99 3434 148 0.1507 0.1720 REMARK 3 3 3.9400 - 3.4400 0.99 3425 146 0.1820 0.2384 REMARK 3 4 3.4400 - 3.1300 0.99 3381 145 0.1981 0.2254 REMARK 3 5 3.1300 - 2.9000 0.99 3388 145 0.2122 0.2437 REMARK 3 6 2.9000 - 2.7300 0.99 3360 144 0.2090 0.2432 REMARK 3 7 2.7300 - 2.6000 0.99 3349 143 0.2121 0.2729 REMARK 3 8 2.6000 - 2.4800 0.98 3338 143 0.2083 0.2646 REMARK 3 9 2.4800 - 2.3900 0.98 3328 143 0.2105 0.2378 REMARK 3 10 2.3900 - 2.3100 0.98 3298 142 0.2090 0.2394 REMARK 3 11 2.3100 - 2.2300 0.99 3325 141 0.2208 0.2713 REMARK 3 12 2.2300 - 2.1700 0.97 3275 141 0.2268 0.2610 REMARK 3 13 2.1700 - 2.1100 0.97 3260 140 0.2667 0.3272 REMARK 3 14 2.1100 - 2.0600 0.87 2921 125 0.3078 0.3326 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) : 0.245 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.173 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 39.98 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 46.04 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 3568 REMARK 3 ANGLE : 1.012 4841 REMARK 3 CHIRALITY : 0.056 514 REMARK 3 PLANARITY : 0.006 629 REMARK 3 DIHEDRAL : 18.781 1304 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 6VCL COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-JAN-20. REMARK 100 THE DEPOSITION ID IS D_1000245149. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 18-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 9.2 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) : 0.9793 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M-F REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48690 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.050 REMARK 200 RESOLUTION RANGE LOW (A) : 30.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 21.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.05 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.09 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 6D1V REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 68.28 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.88 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 30% (V/V) PEG400, 0.1 M CHES, PH 9.2, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291.15K 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 25.66800 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 25.66800 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 81.22200 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 95.32450 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 81.22200 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 95.32450 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 25.66800 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 81.22200 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 95.32450 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 25.66800 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 81.22200 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 95.32450 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: DIMERIC 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 397 LIES ON A SPECIAL POSITION. REMARK 375 HOH B 404 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 160 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 142 CD NE CZ NH1 NH2 REMARK 470 ARG B 85 NE CZ NH1 NH2 REMARK 470 LYS B 89 CG CD CE NZ 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 -140.40 70.82 REMARK 500 GLU A 145 71.63 -107.36 REMARK 500 MET A 155 30.91 -98.79 REMARK 500 THR A 169 55.51 -105.36 REMARK 500 ALA A 171 47.54 -85.01 REMARK 500 ARG A 188 179.37 61.74 REMARK 500 ALA A 216 89.70 -151.46 REMARK 500 MET B 156 36.68 -72.86 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 525 DISTANCE = 6.23 ANGSTROMS REMARK 525 HOH A 526 DISTANCE = 6.82 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 MG B 203 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLN B 37 O REMARK 620 2 GLU B 57 OE2 88.7 REMARK 620 3 GLU B 120 OE1 168.3 83.3 REMARK 620 4 0O2 B 209 O1G 97.9 170.4 91.1 REMARK 620 5 HOH B 361 O 89.2 89.0 82.2 98.0 REMARK 620 N 1 2 3 4 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 304 O 96.9 REMARK 620 3 HOH B 307 O 82.1 88.3 REMARK 620 4 HOH B 357 O 93.8 167.3 100.0 REMARK 620 5 HOH B 405 O 105.4 89.3 172.4 81.3 REMARK 620 6 HOH B 446 O 163.2 91.6 83.8 79.9 89.1 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 57 OE2 82.7 REMARK 620 3 GLU B 120 OE2 156.7 78.4 REMARK 620 4 HOH B 325 O 83.0 101.4 87.4 REMARK 620 5 HOH B 405 O 106.6 157.1 96.0 100.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG B 204 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 0O2 B 209 O2G REMARK 620 2 HOH B 304 O 89.6 REMARK 620 3 HOH B 370 O 100.1 168.9 REMARK 620 4 HOH B 405 O 160.4 78.6 93.4 REMARK 620 5 HOH B 425 O 108.4 89.5 82.3 87.3 REMARK 620 N 1 2 3 4 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 203 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 204 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 205 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue GOL B 206 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue CL B 207 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue F B 208 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 0O2 B 209 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6VCK RELATED DB: PDB REMARK 900 6VCK CONTAINS THE SAME PROTEINS COMPLEXED WITH GDP DBREF 6VCL A 1 274 UNP P0A6K1 DAPF_ECOLI 1 274 DBREF 6VCL B 1 160 UNP P0A776 RPPH_ECOLI 1 160 SEQADV 6VCL SER A 0 UNP P0A6K1 EXPRESSION TAG SEQADV 6VCL ALA A 36 UNP P0A6K1 ARG 36 ENGINEERED MUTATION SEQADV 6VCL ALA A 268 UNP P0A6K1 TYR 268 ENGINEERED MUTATION SEQADV 6VCL SER B 0 UNP P0A776 EXPRESSION TAG SEQADV 6VCL ALA B 159 UNP P0A776 GLN 159 ENGINEERED MUTATION SEQADV 6VCL ALA B 160 UNP P0A776 GLU 160 ENGINEERED MUTATION 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 ALA 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 ALA ASP GLY PHE ILE SEQRES 22 A 275 HIS LEU SEQRES 1 B 161 SER MET ILE ASP ASP ASP GLY TYR ARG PRO ASN VAL GLY SEQRES 2 B 161 ILE VAL ILE CYS ASN ARG GLN GLY GLN VAL MET TRP ALA SEQRES 3 B 161 ARG ARG PHE GLY GLN HIS SER TRP GLN PHE PRO GLN GLY SEQRES 4 B 161 GLY ILE ASN PRO GLY GLU SER ALA GLU GLN ALA MET TYR SEQRES 5 B 161 ARG GLU LEU PHE GLU GLU VAL GLY LEU SER ARG LYS ASP SEQRES 6 B 161 VAL ARG ILE LEU ALA SER THR ARG ASN TRP LEU ARG TYR SEQRES 7 B 161 LYS LEU PRO LYS ARG LEU VAL ARG TRP ASP THR LYS PRO SEQRES 8 B 161 VAL CYS ILE GLY GLN LYS GLN LYS TRP PHE LEU LEU GLN SEQRES 9 B 161 LEU VAL SER GLY ASP ALA GLU ILE ASN MET GLN THR SER SEQRES 10 B 161 SER THR PRO GLU PHE ASP GLY TRP ARG TRP VAL SER TYR SEQRES 11 B 161 TRP TYR PRO VAL ARG GLN VAL VAL SER PHE LYS ARG ASP SEQRES 12 B 161 VAL TYR ARG ARG VAL MET LYS GLU PHE ALA SER VAL VAL SEQRES 13 B 161 MET SER LEU ALA ALA HET CL A 301 1 HET MG B 201 1 HET MG B 202 1 HET MG B 203 1 HET MG B 204 1 HET GOL B 205 14 HET GOL B 206 14 HET CL B 207 1 HET F B 208 1 HET 0O2 B 209 40 HETNAM CL CHLORIDE ION HETNAM MG MAGNESIUM ION HETNAM GOL GLYCEROL HETNAM F FLUORIDE ION HETNAM 0O2 GUANOSINE 5'-(TETRAHYDROGEN TRIPHOSPHATE) 3'- HETNAM 2 0O2 (TRIHYDROGEN DIPHOSPHATE) HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 3 CL 2(CL 1-) FORMUL 4 MG 4(MG 2+) FORMUL 8 GOL 2(C3 H8 O3) FORMUL 11 F F 1- FORMUL 12 0O2 C10 H18 N5 O20 P5 FORMUL 13 HOH *280(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 ALA A 171 SER A 181 1 11 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 MET B 156 1 17 SHEET 1 AA110 GLU A 69 VAL A 70 0 SHEET 2 AA110 PHE A 58 ASN A 64 -1 N ILE A 62 O VAL A 70 SHEET 3 AA110 ASP A 94 THR A 99 1 O SER A 98 N PHE A 58 SHEET 4 AA110 GLY A 102 VAL A 108 -1 O GLY A 102 N THR A 99 SHEET 5 AA110 VAL A 114 ASN A 117 -1 O ARG A 115 N THR A 107 SHEET 6 AA110 LEU A 258 GLY A 262 -1 O MET A 260 N VAL A 116 SHEET 7 AA110 GLY A 245 TRP A 251 -1 N ALA A 250 O TYR A 259 SHEET 8 AA110 GLU A 237 LEU A 242 -1 N VAL A 240 O LEU A 247 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 ARG A 142 0 SHEET 2 AA216 THR A 147 SER A 154 -1 O ILE A 148 N MET A 141 SHEET 3 AA216 PRO A 158 VAL A 164 -1 O VAL A 161 N GLY A 151 SHEET 4 AA216 ASN A 190 LYS A 198 1 O GLY A 192 N ILE A 162 SHEET 5 AA216 HIS A 201 GLU A 208 -1 O ARG A 205 N PHE A 193 SHEET 6 AA216 GLU A 237 LEU A 242 1 O ARG A 239 N ILE A 202 SHEET 7 AA216 GLY A 245 TRP A 251 -1 O LEU A 247 N VAL A 240 SHEET 8 AA216 LEU A 258 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 116 O MET A 260 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 THR A 99 O GLY A 102 SHEET 12 AA216 PHE A 58 ASN A 64 1 N PHE A 58 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 ALA A 268 N LYS A 5 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 VAL B 14 SHEET 4 AA3 4 VAL B 65 SER B 70 -1 N LEU B 68 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 VAL B 14 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 GLN B 21 ARG B 27 -1 N ALA B 25 O GLN B 34 SHEET 3 AA5 3 PHE B 121 SER B 128 -1 O VAL B 127 N VAL B 22 LINK O GLN B 37 MG MG B 203 1555 1555 1.93 LINK OE2 GLU B 53 MG MG B 201 1555 1555 2.00 LINK OE1 GLU B 53 MG MG B 202 1555 1555 2.04 LINK OE2 GLU B 57 MG MG B 202 1555 1555 2.37 LINK OE2 GLU B 57 MG MG B 203 1555 1555 2.12 LINK OE2 GLU B 120 MG MG B 202 1555 1555 2.12 LINK OE1 GLU B 120 MG MG B 203 1555 1555 2.13 LINK MG MG B 201 O HOH B 304 1555 1555 1.98 LINK MG MG B 201 O HOH B 307 1555 1555 2.11 LINK MG MG B 201 O HOH B 357 1555 1555 2.30 LINK MG MG B 201 O HOH B 405 1555 1555 1.91 LINK MG MG B 201 O HOH B 446 1555 1555 2.22 LINK MG MG B 202 O HOH B 325 1555 1555 2.11 LINK MG MG B 202 O HOH B 405 1555 1555 2.06 LINK MG MG B 203 O1G 0O2 B 209 1555 1555 2.06 LINK MG MG B 203 O HOH B 361 1555 1555 2.26 LINK MG MG B 204 O2G 0O2 B 209 1555 1555 1.94 LINK MG MG B 204 O HOH B 304 1555 1555 1.92 LINK MG MG B 204 O HOH B 370 1555 1555 2.10 LINK MG MG B 204 O HOH B 405 1555 1555 2.37 LINK MG MG B 204 O HOH B 425 1555 1555 2.47 CISPEP 1 VAL A 128 PRO A 129 0 -2.19 CISPEP 2 LYS B 89 PRO B 90 0 -8.30 SITE 1 AC1 2 VAL A 105 HOH A 490 SITE 1 AC2 9 GLU B 53 MG B 202 MG B 204 F B 208 SITE 2 AC2 9 HOH B 304 HOH B 307 HOH B 357 HOH B 405 SITE 3 AC2 9 HOH B 446 SITE 1 AC3 9 GLU B 53 GLU B 57 GLU B 120 MG B 201 SITE 2 AC3 9 MG B 203 MG B 204 F B 208 HOH B 325 SITE 3 AC3 9 HOH B 405 SITE 1 AC4 8 GLN B 37 GLU B 57 GLU B 120 MG B 202 SITE 2 AC4 8 MG B 204 F B 208 0O2 B 209 HOH B 361 SITE 1 AC5 9 MG B 201 MG B 202 MG B 203 F B 208 SITE 2 AC5 9 0O2 B 209 HOH B 304 HOH B 370 HOH B 405 SITE 3 AC5 9 HOH B 425 SITE 1 AC6 4 TRP B 74 LEU B 75 ARG B 76 ARG B 146 SITE 1 AC7 4 HIS A 266 VAL A 267 ARG B 26 ASP B 122 SITE 1 AC8 2 SER B 61 ARG B 62 SITE 1 AC9 13 GLN B 37 GLY B 38 GLU B 53 GLU B 57 SITE 2 AC9 13 GLU B 120 MG B 201 MG B 202 MG B 203 SITE 3 AC9 13 MG B 204 0O2 B 209 HOH B 304 HOH B 370 SITE 4 AC9 13 HOH B 405 SITE 1 AD1 26 SER A 68 ARG B 8 ASN B 10 ARG B 27 SITE 2 AD1 26 SER B 32 GLN B 37 GLY B 38 TYR B 77 SITE 3 AD1 26 LEU B 83 GLN B 95 GLU B 120 VAL B 137 SITE 4 AD1 26 PHE B 139 LYS B 140 MG B 203 MG B 204 SITE 5 AD1 26 F B 208 HOH B 303 HOH B 304 HOH B 306 SITE 6 AD1 26 HOH B 317 HOH B 327 HOH B 337 HOH B 340 SITE 7 AD1 26 HOH B 359 HOH B 370 CRYST1 162.444 190.649 51.336 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 0.006156 0.000000 0.000000 0.00000 SCALE2 0.000000 0.005245 0.000000 0.00000 SCALE3 0.000000 0.000000 0.019480 0.00000