HEADER ISOMERASE/HYDROLASE 27-SEP-17 5YGU TITLE CRYSTAL STRUCTURE OF ESCHERICHIA COLI (STRAIN K12) MRNA DECAPPING TITLE 2 COMPLEX RPPH-DAPF 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 MOL_ID: 2; COMPND 8 MOLECULE: RNA PYROPHOSPHOHYDROLASE; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: UNP RESIDUES 1-158; 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 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 11 ORGANISM_TAXID: 83333; SOURCE 12 STRAIN: K12; SOURCE 13 GENE: RPPH, NUDH, YGDP, B2830, JW2798; SOURCE 14 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 15 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 16 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS RPPH-DAPF, DECAPPING, HYDROLASE, ISOMERASE-HYDROLASE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR Q.WANG,Z.Y.GUAN,D.L.ZHANG,T.T.ZOU,P.YIN REVDAT 4 22-NOV-23 5YGU 1 REMARK REVDAT 3 08-AUG-18 5YGU 1 JRNL REVDAT 2 18-JUL-18 5YGU 1 JRNL REVDAT 1 06-JUN-18 5YGU 0 JRNL AUTH Q.WANG,D.ZHANG,Z.GUAN,D.LI,K.PEI,J.LIU,T.ZOU,P.YIN JRNL TITL DAPF STABILIZES THE SUBSTRATE-FAVORING CONFORMATION OF RPPH JRNL TITL 2 TO STIMULATE ITS RNA-PYROPHOSPHOHYDROLASE ACTIVITY IN JRNL TITL 3 ESCHERICHIA COLI. JRNL REF NUCLEIC ACIDS RES. V. 46 6880 2018 JRNL REFN ESSN 1362-4962 JRNL PMID 29931175 JRNL DOI 10.1093/NAR/GKY528 REMARK 2 REMARK 2 RESOLUTION. 2.30 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155) 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) : 2.30 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.99 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 29950 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.208 REMARK 3 R VALUE (WORKING SET) : 0.206 REMARK 3 FREE R VALUE : 0.239 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.050 REMARK 3 FREE R VALUE TEST SET COUNT : 1513 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 47.9958 - 5.1080 0.98 2756 153 0.2073 0.2133 REMARK 3 2 5.1080 - 4.0551 1.00 2649 147 0.1609 0.1790 REMARK 3 3 4.0551 - 3.5427 1.00 2629 126 0.1881 0.2300 REMARK 3 4 3.5427 - 3.2188 1.00 2545 155 0.2060 0.2723 REMARK 3 5 3.2188 - 2.9882 1.00 2590 141 0.2434 0.2803 REMARK 3 6 2.9882 - 2.8120 1.00 2572 124 0.2387 0.2647 REMARK 3 7 2.8120 - 2.6712 1.00 2573 128 0.2459 0.2987 REMARK 3 8 2.6712 - 2.5549 1.00 2551 123 0.2408 0.3028 REMARK 3 9 2.5549 - 2.4566 1.00 2560 128 0.2374 0.3284 REMARK 3 10 2.4566 - 2.3718 1.00 2536 150 0.2558 0.3158 REMARK 3 11 2.3718 - 2.2976 0.99 2476 138 0.2699 0.3393 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) : 0.290 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.400 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 : 0.009 3433 REMARK 3 ANGLE : 1.030 4643 REMARK 3 CHIRALITY : 0.057 500 REMARK 3 PLANARITY : 0.007 607 REMARK 3 DIHEDRAL : 25.551 1257 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 4.2964 5.6066 21.3458 REMARK 3 T TENSOR REMARK 3 T11: 0.5601 T22: 0.3763 REMARK 3 T33: 0.3487 T12: -0.0659 REMARK 3 T13: 0.0827 T23: 0.0164 REMARK 3 L TENSOR REMARK 3 L11: 1.2135 L22: 2.1666 REMARK 3 L33: 1.2430 L12: -0.1188 REMARK 3 L13: 0.2274 L23: 0.1131 REMARK 3 S TENSOR REMARK 3 S11: 0.0652 S12: -0.2333 S13: -0.1831 REMARK 3 S21: 0.6510 S22: -0.0956 S23: 0.4041 REMARK 3 S31: 0.2083 S32: -0.2262 S33: 0.0186 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 5YGU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 02-OCT-17. REMARK 100 THE DEPOSITION ID IS D_1300005172. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 03-JAN-15 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 : SSRF REMARK 200 BEAMLINE : BL17U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9792 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 30026 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.290 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 14.00 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.8000 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 4S2V, 4IJZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.21 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: POTASSIUM SODIUM TARTRATE, SODIUM REMARK 280 IODINE, XYLITOL, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 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 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 86.54650 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 43.20900 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 43.20900 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 43.27325 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 43.20900 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 43.20900 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 129.81975 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 43.20900 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 43.20900 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 43.27325 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 43.20900 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 43.20900 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 129.81975 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 86.54650 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: 3540 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19890 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -10.0 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 ASP B 4 REMARK 465 GLY B 43 REMARK 465 GLU B 44 REMARK 465 ASN B 73 REMARK 465 SER B 117 REMARK 465 THR B 118 REMARK 465 PRO B 119 REMARK 465 GLU B 120 REMARK 465 LEU B 159 REMARK 465 GLU B 160 REMARK 465 HIS B 161 REMARK 465 HIS B 162 REMARK 465 HIS B 163 REMARK 465 HIS B 164 REMARK 465 HIS B 165 REMARK 465 HIS B 166 REMARK 465 HIS B 167 REMARK 465 HIS B 168 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 LYS A 198 CE NZ REMARK 470 LYS B 63 CG CD CE NZ REMARK 470 ASP B 64 CG OD1 OD2 REMARK 470 ARG B 72 CG CD NE CZ NH1 NH2 REMARK 470 GLU B 110 CG CD OE1 OE2 REMARK 470 PHE B 121 CG CD1 CD2 CE1 CE2 CZ REMARK 470 ARG B 134 CG CD NE CZ NH1 NH2 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 NH2 ARG B 66 OE1 GLN B 103 1.89 REMARK 500 OE1 GLU A 136 O HOH A 401 1.90 REMARK 500 O HOH A 438 O HOH A 445 1.91 REMARK 500 O VAL B 136 NH1 ARG B 141 1.92 REMARK 500 O HOH A 451 O HOH A 454 2.01 REMARK 500 I IOD A 303 O HOH A 460 2.04 REMARK 500 O HOH A 431 O HOH A 457 2.04 REMARK 500 OG1 THR A 109 OD1 ASP A 111 2.09 REMARK 500 OE2 GLU A 241 O HOH A 402 2.13 REMARK 500 O ASP B 3 N ASP B 5 2.19 REMARK 500 REMARK 500 REMARK: NULL 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 ARG A 142 NE - CZ - NH2 ANGL. DEV. = -3.0 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 LYS A 134 172.61 170.80 REMARK 500 ALA A 144 -128.43 50.78 REMARK 500 ARG A 188 -179.42 72.97 REMARK 500 VAL A 197 -62.67 -93.46 REMARK 500 HIS A 273 80.00 -100.68 REMARK 500 ILE B 2 37.09 -91.71 REMARK 500 SER B 16 -168.89 -78.87 REMARK 500 ASP B 64 -10.08 106.40 REMARK 500 LYS B 81 -59.15 -25.27 REMARK 500 SER B 106 -58.52 -120.62 REMARK 500 MET B 113 1.34 -68.33 REMARK 500 GLN B 114 146.17 172.52 REMARK 500 THR B 115 -167.52 65.29 REMARK 500 ASP B 122 -80.97 163.74 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 TLA A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 308 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 309 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD A 310 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD B 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue IOD B 202 DBREF 5YGU A 1 274 UNP P0A6K1 DAPF_ECOLI 1 274 DBREF 5YGU B 1 158 UNP P0A776 RPPH_ECOLI 1 158 SEQADV 5YGU SER B 16 UNP P0A776 CYS 16 ENGINEERED MUTATION SEQADV 5YGU LEU B 159 UNP P0A776 EXPRESSION TAG SEQADV 5YGU GLU B 160 UNP P0A776 EXPRESSION TAG SEQADV 5YGU HIS B 161 UNP P0A776 EXPRESSION TAG SEQADV 5YGU HIS B 162 UNP P0A776 EXPRESSION TAG SEQADV 5YGU HIS B 163 UNP P0A776 EXPRESSION TAG SEQADV 5YGU HIS B 164 UNP P0A776 EXPRESSION TAG SEQADV 5YGU HIS B 165 UNP P0A776 EXPRESSION TAG SEQADV 5YGU HIS B 166 UNP P0A776 EXPRESSION TAG SEQADV 5YGU HIS B 167 UNP P0A776 EXPRESSION TAG SEQADV 5YGU HIS B 168 UNP P0A776 EXPRESSION TAG SEQRES 1 A 274 MET GLN PHE SER LYS MET HIS GLY LEU GLY ASN ASP PHE SEQRES 2 A 274 MET VAL VAL ASP ALA VAL THR GLN ASN VAL PHE PHE SER SEQRES 3 A 274 PRO GLU LEU ILE ARG ARG LEU ALA ASP ARG HIS LEU GLY SEQRES 4 A 274 VAL GLY PHE ASP GLN LEU LEU VAL VAL GLU PRO PRO TYR SEQRES 5 A 274 ASP PRO GLU LEU ASP PHE HIS TYR ARG ILE PHE ASN ALA SEQRES 6 A 274 ASP GLY SER GLU VAL ALA GLN CYS GLY ASN GLY ALA ARG SEQRES 7 A 274 CYS PHE ALA ARG PHE VAL ARG LEU LYS GLY LEU THR ASN SEQRES 8 A 274 LYS ARG ASP ILE ARG VAL SER THR ALA ASN GLY ARG MET SEQRES 9 A 274 VAL LEU THR VAL THR ASP ASP ASP LEU VAL ARG VAL ASN SEQRES 10 A 274 MET GLY GLU PRO ASN PHE GLU PRO SER ALA VAL PRO PHE SEQRES 11 A 274 ARG ALA ASN LYS ALA GLU LYS THR TYR ILE MET ARG ALA SEQRES 12 A 274 ALA GLU GLN THR ILE LEU CYS GLY VAL VAL SER MET GLY SEQRES 13 A 274 ASN PRO HIS CYS VAL ILE GLN VAL ASP ASP VAL ASP THR SEQRES 14 A 274 ALA ALA VAL GLU THR LEU GLY PRO VAL LEU GLU SER HIS SEQRES 15 A 274 GLU ARG PHE PRO GLU ARG ALA ASN ILE GLY PHE MET GLN SEQRES 16 A 274 VAL VAL LYS ARG GLU HIS ILE ARG LEU ARG VAL TYR GLU SEQRES 17 A 274 ARG GLY ALA GLY GLU THR GLN ALA CYS GLY SER GLY ALA SEQRES 18 A 274 CYS ALA ALA VAL ALA VAL GLY ILE GLN GLN GLY LEU LEU SEQRES 19 A 274 ALA GLU GLU VAL ARG VAL GLU LEU PRO GLY GLY ARG LEU SEQRES 20 A 274 ASP ILE ALA TRP LYS GLY PRO GLY HIS PRO LEU TYR MET SEQRES 21 A 274 THR GLY PRO ALA VAL HIS VAL TYR ASP GLY PHE ILE HIS SEQRES 22 A 274 LEU SEQRES 1 B 168 MET ILE ASP ASP ASP GLY TYR ARG PRO ASN VAL GLY ILE SEQRES 2 B 168 VAL ILE SER ASN ARG GLN GLY GLN VAL MET TRP ALA ARG SEQRES 3 B 168 ARG PHE GLY GLN HIS SER TRP GLN PHE PRO GLN GLY GLY SEQRES 4 B 168 ILE ASN PRO GLY GLU SER ALA GLU GLN ALA MET TYR ARG SEQRES 5 B 168 GLU LEU PHE GLU GLU VAL GLY LEU SER ARG LYS ASP VAL SEQRES 6 B 168 ARG ILE LEU ALA SER THR ARG ASN TRP LEU ARG TYR LYS SEQRES 7 B 168 LEU PRO LYS ARG LEU VAL ARG TRP ASP THR LYS PRO VAL SEQRES 8 B 168 CYS ILE GLY GLN LYS GLN LYS TRP PHE LEU LEU GLN LEU SEQRES 9 B 168 VAL SER GLY ASP ALA GLU ILE ASN MET GLN THR SER SER SEQRES 10 B 168 THR PRO GLU PHE ASP GLY TRP ARG TRP VAL SER TYR TRP SEQRES 11 B 168 TYR PRO VAL ARG GLN VAL VAL SER PHE LYS ARG ASP VAL SEQRES 12 B 168 TYR ARG ARG VAL MET LYS GLU PHE ALA SER VAL VAL MET SEQRES 13 B 168 SER LEU LEU GLU HIS HIS HIS HIS HIS HIS HIS HIS HET TLA A 301 10 HET IOD A 302 1 HET IOD A 303 1 HET IOD A 304 1 HET IOD A 305 1 HET IOD A 306 1 HET IOD A 307 1 HET IOD A 308 1 HET IOD A 309 1 HET IOD A 310 1 HET IOD A 311 1 HET IOD B 201 1 HET IOD B 202 1 HETNAM TLA L(+)-TARTARIC ACID HETNAM IOD IODIDE ION FORMUL 3 TLA C4 H6 O6 FORMUL 4 IOD 12(I 1-) FORMUL 16 HOH *79(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 ALA B 46 GLY B 59 1 14 HELIX 7 AA7 PRO B 80 VAL B 84 5 5 HELIX 8 AA8 GLY B 107 ILE B 111 5 5 HELIX 9 AA9 TRP B 130 VAL B 136 1 7 HELIX 10 AB1 VAL B 137 PHE B 139 5 3 HELIX 11 AB2 LYS B 140 SER B 157 1 18 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 TYR A 259 GLY A 262 -1 O MET A 260 N VAL A 116 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 VAL A 240 O LEU A 247 SHEET 9 AA110 HIS A 201 GLU A 208 1 N ILE A 202 O GLU A 241 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 GLN A 146 N ALA A 143 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 GLY A 192 N CYS A 160 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 GLU A 241 N ILE A 202 SHEET 7 AA216 GLY A 245 ALA A 250 -1 O LEU A 247 N VAL A 240 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 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 VAL A 47 O ARG A 61 SHEET 14 AA216 ASN A 11 ASP A 17 1 N MET A 14 O LEU A 46 SHEET 15 AA216 GLN A 2 GLY A 8 -1 N MET A 6 O PHE A 13 SHEET 16 AA216 VAL A 265 PHE A 271 -1 O GLY A 270 N PHE A 3 SHEET 1 AA3 4 GLN B 37 GLY B 39 0 SHEET 2 AA3 4 TYR B 7 SER 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 SER B 16 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 SER 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 SER B 16 SHEET 4 AA4 4 LEU B 75 LYS B 78 -1 N TYR B 77 O GLN B 95 SHEET 1 AA5 3 TRP B 33 GLN B 34 0 SHEET 2 AA5 3 VAL B 22 ARG B 26 -1 N ALA B 25 O GLN B 34 SHEET 3 AA5 3 TRP B 124 VAL B 127 -1 O ARG B 125 N TRP B 24 CISPEP 1 VAL A 128 PRO A 129 0 -6.31 CISPEP 2 MET B 1 ILE B 2 0 1.00 CISPEP 3 LYS B 89 PRO B 90 0 -2.18 CISPEP 4 GLN B 114 THR B 115 0 -8.81 SITE 1 AC1 9 GLN A 72 ASN A 157 ASN A 190 GLU A 208 SITE 2 AC1 9 ARG A 209 CYS A 217 SER A 219 HOH A 404 SITE 3 AC1 9 HOH A 420 SITE 1 AC2 1 HOH A 460 SITE 1 AC3 1 HIS A 201 SITE 1 AC4 1 ASN A 133 SITE 1 AC5 1 GLU A 69 SITE 1 AC6 2 ASN A 11 ARG A 78 SITE 1 AC7 2 ARG A 82 ARG A 85 SITE 1 AC8 2 THR A 99 ASN A 101 SITE 1 AC9 1 ARG B 134 SITE 1 AD1 1 GLN B 95 CRYST1 86.418 86.418 173.093 90.00 90.00 90.00 P 41 21 2 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 0.011572 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011572 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005777 0.00000