HEADER LYASE 04-JUN-20 6Z9H TITLE ESCHERICHIA COLI D-2-DEOXYRIBOSE-5-PHOSPHATE ALDOLASE - TITLE 2 C47V/G204A/S239D MUTANT COMPND MOL_ID: 1; COMPND 2 MOLECULE: DEOXYRIBOSE-PHOSPHATE ALDOLASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: DERA,2-DEOXY-D-RIBOSE 5-PHOSPHATE ALDOLASE, COMPND 5 PHOSPHODEOXYRIBOALDOLASE,DEOXYRIBOALDOLASE; COMPND 6 EC: 4.1.2.4; COMPND 7 ENGINEERED: YES; COMPND 8 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: DEOC, A6592_04055, A9819_24930, AJ318_04090, AML35_20375, SOURCE 5 AWE53_009755, AWF59_004780, AWG90_001355, AZZ83_003140, B9M99_13055, SOURCE 6 BHF46_08905, BIU72_19175, BIZ41_21315, BK292_12675, BK296_03525, SOURCE 7 BK375_05655, BON91_08010, BVCMSC61A_04176, BVCMSHHP001_01002, SOURCE 8 BVCMSKKP061_00143, BVCMSKSP045_01273, BVCMSKSP067_04018, SOURCE 9 BVCMSKSP076_01350, BVCMSNSP047_00091, BVCMSSINP022_00140, SOURCE 10 BZL69_04490, C4M78_04295, C7B08_10715, C7B18_26170, CDC27_23655, SOURCE 11 D2188_24830, D3P01_08005, D9D31_02570, D9E34_05115, D9G48_24275, SOURCE 12 D9I87_14825, D9I88_23755, D9K54_15785, DD762_00045, DND16_14490, SOURCE 13 DNQ45_13620, DTL90_19480, DTM45_25725, DU321_02660, DXT71_19415, SOURCE 14 E0L12_12025, E5S46_05005, E5S58_22595, E5S61_04910, EC382_07685, SOURCE 15 EL79_3891, EL80_3836, ELT23_13160, ELV08_18870, ELV15_04550, SOURCE 16 ELV28_15080, EQ825_04285, EQ830_02895, ERS085386_00787, EVY14_13465, SOURCE 17 EXX13_04350, EXX23_12990, EXX53_09895, EYY34_19360, FNJ83_01355, SOURCE 18 FV438_05665, FWK02_17600, FY127_22350, HMPREF3040_02396, SOURCE 19 NCTC10090_02419, NCTC7922_05561, NCTC9117_05294, NCTC9777_00681, SOURCE 20 NCTC9969_04462, PGD_03624, SAMEA3472056_01168, SAMEA3472108_04807, SOURCE 21 SAMEA3485101_00909, SAMEA3485113_03629, SAMEA3752559_04076, SOURCE 22 SAMEA3753300_03100, UC41_15640; SOURCE 23 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 24 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 25 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 26 EXPRESSION_SYSTEM_PLASMID: PBAT4 KEYWDS ALDOLASE, LYASE, DERA EXPDTA X-RAY DIFFRACTION AUTHOR J.PAAKKONEN,N.HAKULINEN,J.ROUVINEN REVDAT 3 24-JAN-24 6Z9H 1 REMARK REVDAT 2 25-NOV-20 6Z9H 1 JRNL REVDAT 1 18-NOV-20 6Z9H 0 JRNL AUTH S.VOUTILAINEN,M.HEINONEN,M.ANDBERG,E.JOKINEN,H.MAAHEIMO, JRNL AUTH 2 J.PAAKKONEN,N.HAKULINEN,J.ROUVINEN,H.LAHDESMAKI,S.KASKI, JRNL AUTH 3 J.ROUSU,M.PENTTILA,A.KOIVULA JRNL TITL SUBSTRATE SPECIFICITY OF 2-DEOXY-D-RIBOSE 5-PHOSPHATE JRNL TITL 2 ALDOLASE (DERA) ASSESSED BY DIFFERENT PROTEIN ENGINEERING JRNL TITL 3 AND MACHINE LEARNING METHODS. JRNL REF APPL.MICROBIOL.BIOTECHNOL. V. 104 10515 2020 JRNL REFN ESSN 1432-0614 JRNL PMID 33147349 JRNL DOI 10.1007/S00253-020-10960-X REMARK 2 REMARK 2 RESOLUTION. 1.72 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.13_2998 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 : GEOSTD + MONOMER LIBRARY REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.72 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 38.35 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.8 REMARK 3 NUMBER OF REFLECTIONS : 51130 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.184 REMARK 3 R VALUE (WORKING SET) : 0.182 REMARK 3 FREE R VALUE : 0.227 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.840 REMARK 3 FREE R VALUE TEST SET COUNT : 2476 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 38.3500 - 4.5100 0.98 2836 144 0.1248 0.1403 REMARK 3 2 4.5100 - 3.5800 0.99 2789 142 0.1176 0.1442 REMARK 3 3 3.5800 - 3.1200 0.98 2745 143 0.1481 0.1918 REMARK 3 4 3.1200 - 2.8400 0.97 2711 146 0.1815 0.2379 REMARK 3 5 2.8400 - 2.6400 0.96 2728 107 0.1924 0.2221 REMARK 3 6 2.6400 - 2.4800 0.96 2664 133 0.2175 0.2861 REMARK 3 7 2.4800 - 2.3600 0.96 2677 146 0.2240 0.2802 REMARK 3 8 2.3600 - 2.2500 0.97 2708 130 0.2119 0.2834 REMARK 3 9 2.2500 - 2.1700 0.96 2672 151 0.2159 0.2790 REMARK 3 10 2.1700 - 2.0900 0.96 2685 137 0.2300 0.2824 REMARK 3 11 2.0900 - 2.0300 0.95 2659 132 0.2204 0.2874 REMARK 3 12 2.0300 - 1.9700 0.96 2653 147 0.2208 0.2713 REMARK 3 13 1.9700 - 1.9200 0.96 2662 124 0.2153 0.2626 REMARK 3 14 1.9200 - 1.8700 0.96 2654 148 0.2183 0.2815 REMARK 3 15 1.8700 - 1.8300 0.97 2705 133 0.2280 0.2775 REMARK 3 16 1.8300 - 1.7900 0.97 2684 135 0.2426 0.2949 REMARK 3 17 1.7900 - 1.7500 0.97 2709 136 0.2621 0.2867 REMARK 3 18 1.7500 - 1.7200 0.98 2713 142 0.2964 0.3816 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.254 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.496 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.14 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 23.58 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 3836 REMARK 3 ANGLE : 0.944 5199 REMARK 3 CHIRALITY : 0.057 620 REMARK 3 PLANARITY : 0.006 677 REMARK 3 DIHEDRAL : 12.881 2362 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 6Z9H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1292108818. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-JUL-19 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I24 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9688 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AUTOPROC, XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 51138 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.580 REMARK 200 RESOLUTION RANGE LOW (A) : 39.410 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 200 DATA REDUNDANCY : 1.760 REMARK 200 R MERGE (I) : 0.08700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.72 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.78 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.46200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.100 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: 1KTN REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.91 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.19 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, MAGNESIUM FORMATE, BIS-TRIS, REMARK 280 PH 6.5, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K 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 26.93500 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A 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 350 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 MET A -6 REMARK 465 ALA A -5 REMARK 465 HIS A -4 REMARK 465 HIS A -3 REMARK 465 HIS A -2 REMARK 465 HIS A -1 REMARK 465 HIS A 0 REMARK 465 HIS A 1 REMARK 465 THR A 2 REMARK 465 GLY A 251 REMARK 465 ASP A 252 REMARK 465 GLY A 253 REMARK 465 LYS A 254 REMARK 465 SER A 255 REMARK 465 ALA A 256 REMARK 465 SER A 257 REMARK 465 SER A 258 REMARK 465 TYR A 259 REMARK 465 MET B -6 REMARK 465 ALA B -5 REMARK 465 HIS B -4 REMARK 465 HIS B -3 REMARK 465 HIS B -2 REMARK 465 HIS B -1 REMARK 465 HIS B 0 REMARK 465 HIS B 1 REMARK 465 THR B 2 REMARK 465 GLY B 251 REMARK 465 ASP B 252 REMARK 465 GLY B 253 REMARK 465 LYS B 254 REMARK 465 SER B 255 REMARK 465 ALA B 256 REMARK 465 SER B 257 REMARK 465 SER B 258 REMARK 465 TYR B 259 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 196 CD CE NZ 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 O HOH B 554 O HOH B 605 1.88 REMARK 500 O HOH A 420 O HOH A 538 1.96 REMARK 500 NH1 ARG A 108 O HOH A 401 2.03 REMARK 500 O HOH B 403 O HOH B 568 2.05 REMARK 500 OD1 ASP A 147 O HOH A 402 2.12 REMARK 500 O HOH A 410 O HOH B 467 2.15 REMARK 500 O HOH B 572 O HOH B 617 2.17 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 O HOH B 525 O HOH B 657 2545 2.18 REMARK 500 O HOH B 546 O HOH B 573 2555 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 GLU A 141 64.43 60.89 REMARK 500 LYS A 146 -57.41 69.18 REMARK 500 ASN A 176 -133.08 -117.27 REMARK 500 ALA A 204 -17.52 73.45 REMARK 500 ASP A 239 -13.63 -144.65 REMARK 500 GLU B 141 67.36 63.09 REMARK 500 LYS B 146 -58.08 67.68 REMARK 500 ASN B 176 -139.85 -116.70 REMARK 500 ALA B 204 -1.25 76.77 REMARK 500 ASP B 239 45.75 -140.34 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 697 DISTANCE = 6.68 ANGSTROMS 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 EDO A 301 REMARK 610 EDO B 301 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 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 402 O REMARK 620 2 HOH B 444 O 112.4 REMARK 620 3 HOH B 524 O 101.0 94.2 REMARK 620 4 HOH B 609 O 75.9 168.8 76.5 REMARK 620 5 HOH B 663 O 77.8 103.9 161.0 84.9 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 EDO A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FMT A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for Di-peptide EDO B 301 and LYS B REMARK 800 167 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1KTN RELATED DB: PDB REMARK 900 INITIAL MODEL FOR REFINEMENT REMARK 900 RELATED ID: 1JCL RELATED DB: PDB REMARK 900 HIGH-RESOLUTION MODEL OF THE WILD-TYPE REMARK 900 RELATED ID: 1JCJ RELATED DB: PDB REMARK 900 HIGH-RESOLUTION MODEL OF THE WILD-TYPE REMARK 900 RELATED ID: 1P1X RELATED DB: PDB REMARK 900 HIGH-RESOLUTION MODEL OF THE WILD-TYPE DBREF 6Z9H A 2 259 UNP E2QLE1 E2QLE1_ECOLX 2 259 DBREF 6Z9H B 2 259 UNP E2QLE1 E2QLE1_ECOLX 2 259 SEQADV 6Z9H MET A -6 UNP E2QLE1 INITIATING METHIONINE SEQADV 6Z9H ALA A -5 UNP E2QLE1 EXPRESSION TAG SEQADV 6Z9H HIS A -4 UNP E2QLE1 EXPRESSION TAG SEQADV 6Z9H HIS A -3 UNP E2QLE1 EXPRESSION TAG SEQADV 6Z9H HIS A -2 UNP E2QLE1 EXPRESSION TAG SEQADV 6Z9H HIS A -1 UNP E2QLE1 EXPRESSION TAG SEQADV 6Z9H HIS A 0 UNP E2QLE1 EXPRESSION TAG SEQADV 6Z9H HIS A 1 UNP E2QLE1 EXPRESSION TAG SEQADV 6Z9H VAL A 47 UNP E2QLE1 CYS 47 ENGINEERED MUTATION SEQADV 6Z9H ALA A 204 UNP E2QLE1 GLY 204 ENGINEERED MUTATION SEQADV 6Z9H ASP A 239 UNP E2QLE1 SER 239 ENGINEERED MUTATION SEQADV 6Z9H MET B -6 UNP E2QLE1 INITIATING METHIONINE SEQADV 6Z9H ALA B -5 UNP E2QLE1 EXPRESSION TAG SEQADV 6Z9H HIS B -4 UNP E2QLE1 EXPRESSION TAG SEQADV 6Z9H HIS B -3 UNP E2QLE1 EXPRESSION TAG SEQADV 6Z9H HIS B -2 UNP E2QLE1 EXPRESSION TAG SEQADV 6Z9H HIS B -1 UNP E2QLE1 EXPRESSION TAG SEQADV 6Z9H HIS B 0 UNP E2QLE1 EXPRESSION TAG SEQADV 6Z9H HIS B 1 UNP E2QLE1 EXPRESSION TAG SEQADV 6Z9H VAL B 47 UNP E2QLE1 CYS 47 ENGINEERED MUTATION SEQADV 6Z9H ALA B 204 UNP E2QLE1 GLY 204 ENGINEERED MUTATION SEQADV 6Z9H ASP B 239 UNP E2QLE1 SER 239 ENGINEERED MUTATION SEQRES 1 A 266 MET ALA HIS HIS HIS HIS HIS HIS THR ASP LEU LYS ALA SEQRES 2 A 266 SER SER LEU ARG ALA LEU LYS LEU MET ASP LEU THR THR SEQRES 3 A 266 LEU ASN ASP ASP ASP THR ASP GLU LYS VAL ILE ALA LEU SEQRES 4 A 266 CYS HIS GLN ALA LYS THR PRO VAL GLY ASN THR ALA ALA SEQRES 5 A 266 ILE VAL ILE TYR PRO ARG PHE ILE PRO ILE ALA ARG LYS SEQRES 6 A 266 THR LEU LYS GLU GLN GLY THR PRO GLU ILE ARG ILE ALA SEQRES 7 A 266 THR VAL THR ASN PHE PRO HIS GLY ASN ASP ASP ILE ASP SEQRES 8 A 266 ILE ALA LEU ALA GLU THR ARG ALA ALA ILE ALA TYR GLY SEQRES 9 A 266 ALA ASP GLU VAL ASP VAL VAL PHE PRO TYR ARG ALA LEU SEQRES 10 A 266 MET ALA GLY ASN GLU GLN VAL GLY PHE ASP LEU VAL LYS SEQRES 11 A 266 ALA CYS LYS GLU ALA CYS ALA ALA ALA ASN VAL LEU LEU SEQRES 12 A 266 LYS VAL ILE ILE GLU THR GLY GLU LEU LYS ASP GLU ALA SEQRES 13 A 266 LEU ILE ARG LYS ALA SER GLU ILE SER ILE LYS ALA GLY SEQRES 14 A 266 ALA ASP PHE ILE LYS THR SER THR GLY LYS VAL ALA VAL SEQRES 15 A 266 ASN ALA THR PRO GLU SER ALA ARG ILE MET MET GLU VAL SEQRES 16 A 266 ILE ARG ASP MET GLY VAL GLU LYS THR VAL GLY PHE LYS SEQRES 17 A 266 PRO ALA ALA GLY VAL ARG THR ALA GLU ASP ALA GLN LYS SEQRES 18 A 266 TYR LEU ALA ILE ALA ASP GLU LEU PHE GLY ALA ASP TRP SEQRES 19 A 266 ALA ASP ALA ARG HIS TYR ARG PHE GLY ALA SER ASP LEU SEQRES 20 A 266 LEU ALA SER LEU LEU LYS ALA LEU GLY HIS GLY ASP GLY SEQRES 21 A 266 LYS SER ALA SER SER TYR SEQRES 1 B 266 MET ALA HIS HIS HIS HIS HIS HIS THR ASP LEU LYS ALA SEQRES 2 B 266 SER SER LEU ARG ALA LEU LYS LEU MET ASP LEU THR THR SEQRES 3 B 266 LEU ASN ASP ASP ASP THR ASP GLU LYS VAL ILE ALA LEU SEQRES 4 B 266 CYS HIS GLN ALA LYS THR PRO VAL GLY ASN THR ALA ALA SEQRES 5 B 266 ILE VAL ILE TYR PRO ARG PHE ILE PRO ILE ALA ARG LYS SEQRES 6 B 266 THR LEU LYS GLU GLN GLY THR PRO GLU ILE ARG ILE ALA SEQRES 7 B 266 THR VAL THR ASN PHE PRO HIS GLY ASN ASP ASP ILE ASP SEQRES 8 B 266 ILE ALA LEU ALA GLU THR ARG ALA ALA ILE ALA TYR GLY SEQRES 9 B 266 ALA ASP GLU VAL ASP VAL VAL PHE PRO TYR ARG ALA LEU SEQRES 10 B 266 MET ALA GLY ASN GLU GLN VAL GLY PHE ASP LEU VAL LYS SEQRES 11 B 266 ALA CYS LYS GLU ALA CYS ALA ALA ALA ASN VAL LEU LEU SEQRES 12 B 266 LYS VAL ILE ILE GLU THR GLY GLU LEU LYS ASP GLU ALA SEQRES 13 B 266 LEU ILE ARG LYS ALA SER GLU ILE SER ILE LYS ALA GLY SEQRES 14 B 266 ALA ASP PHE ILE LYS THR SER THR GLY LYS VAL ALA VAL SEQRES 15 B 266 ASN ALA THR PRO GLU SER ALA ARG ILE MET MET GLU VAL SEQRES 16 B 266 ILE ARG ASP MET GLY VAL GLU LYS THR VAL GLY PHE LYS SEQRES 17 B 266 PRO ALA ALA GLY VAL ARG THR ALA GLU ASP ALA GLN LYS SEQRES 18 B 266 TYR LEU ALA ILE ALA ASP GLU LEU PHE GLY ALA ASP TRP SEQRES 19 B 266 ALA ASP ALA ARG HIS TYR ARG PHE GLY ALA SER ASP LEU SEQRES 20 B 266 LEU ALA SER LEU LEU LYS ALA LEU GLY HIS GLY ASP GLY SEQRES 21 B 266 LYS SER ALA SER SER TYR HET EDO A 301 2 HET FMT A 302 3 HET EDO B 301 2 HET MG B 302 1 HETNAM EDO 1,2-ETHANEDIOL HETNAM FMT FORMIC ACID HETNAM MG MAGNESIUM ION HETSYN EDO ETHYLENE GLYCOL FORMUL 3 EDO 2(C2 H6 O2) FORMUL 4 FMT C H2 O2 FORMUL 6 MG MG 2+ FORMUL 7 HOH *576(H2 O) HELIX 1 AA1 ASP A 3 LEU A 14 1 12 HELIX 2 AA2 THR A 25 ALA A 36 1 12 HELIX 3 AA3 TYR A 49 ARG A 51 5 3 HELIX 4 AA4 PHE A 52 GLN A 63 1 12 HELIX 5 AA5 ASP A 82 GLY A 97 1 16 HELIX 6 AA6 PRO A 106 ALA A 112 1 7 HELIX 7 AA7 GLU A 115 ALA A 132 1 18 HELIX 8 AA8 GLU A 141 LYS A 146 1 6 HELIX 9 AA9 ASP A 147 GLY A 162 1 16 HELIX 10 AB1 THR A 178 GLY A 193 1 16 HELIX 11 AB2 THR A 208 GLY A 224 1 17 HELIX 12 AB3 LEU A 240 LEU A 248 1 9 HELIX 13 AB4 LEU B 4 LEU B 14 1 11 HELIX 14 AB5 THR B 25 ALA B 36 1 12 HELIX 15 AB6 TYR B 49 ARG B 51 5 3 HELIX 16 AB7 PHE B 52 GLN B 63 1 12 HELIX 17 AB8 ASP B 82 GLY B 97 1 16 HELIX 18 AB9 PRO B 106 ALA B 112 1 7 HELIX 19 AC1 GLU B 115 ALA B 132 1 18 HELIX 20 AC2 GLU B 141 LYS B 146 1 6 HELIX 21 AC3 ASP B 147 GLY B 162 1 16 HELIX 22 AC4 THR B 178 GLY B 193 1 16 HELIX 23 AC5 THR B 208 GLY B 224 1 17 HELIX 24 AC6 LEU B 240 LEU B 248 1 9 SHEET 1 AA1 8 GLY A 199 LYS A 201 0 SHEET 2 AA1 8 PHE A 165 LYS A 167 1 N ILE A 166 O GLY A 199 SHEET 3 AA1 8 LEU A 135 ILE A 139 1 N VAL A 138 O LYS A 167 SHEET 4 AA1 8 GLU A 100 VAL A 104 1 N VAL A 101 O LYS A 137 SHEET 5 AA1 8 ARG A 69 THR A 74 1 N THR A 72 O ASP A 102 SHEET 6 AA1 8 ALA A 45 ILE A 48 1 N ILE A 46 O ALA A 71 SHEET 7 AA1 8 MET A 15 THR A 18 1 N LEU A 17 O VAL A 47 SHEET 8 AA1 8 PHE A 235 ALA A 237 1 O PHE A 235 N ASP A 16 SHEET 1 AA2 2 LYS A 37 THR A 38 0 SHEET 2 AA2 2 GLY A 41 ASN A 42 -1 O GLY A 41 N THR A 38 SHEET 1 AA3 8 GLY B 199 LYS B 201 0 SHEET 2 AA3 8 PHE B 165 LYS B 167 1 N ILE B 166 O GLY B 199 SHEET 3 AA3 8 LEU B 135 ILE B 139 1 N VAL B 138 O LYS B 167 SHEET 4 AA3 8 GLU B 100 VAL B 104 1 N VAL B 103 O ILE B 139 SHEET 5 AA3 8 ARG B 69 THR B 74 1 N THR B 72 O ASP B 102 SHEET 6 AA3 8 ALA B 45 VAL B 47 1 N ILE B 46 O ALA B 71 SHEET 7 AA3 8 MET B 15 THR B 18 1 N LEU B 17 O VAL B 47 SHEET 8 AA3 8 PHE B 235 ALA B 237 1 O PHE B 235 N ASP B 16 SHEET 1 AA4 2 LYS B 37 THR B 38 0 SHEET 2 AA4 2 GLY B 41 ASN B 42 -1 O GLY B 41 N THR B 38 LINK NZ LYS A 167 C1 EDO A 301 1555 1555 1.34 LINK NZ LYS B 167 C1 EDO B 301 1555 1555 1.34 LINK MG MG B 302 O HOH B 402 1555 2555 2.42 LINK MG MG B 302 O HOH B 444 1555 1555 2.14 LINK MG MG B 302 O HOH B 524 1555 1555 2.34 LINK MG MG B 302 O HOH B 609 1555 2555 1.98 LINK MG MG B 302 O HOH B 663 1555 2555 2.39 CISPEP 1 PHE A 76 PRO A 77 0 1.35 CISPEP 2 PHE B 76 PRO B 77 0 1.26 SITE 1 AC1 4 LYS A 167 SER A 169 THR A 170 HOH A 586 SITE 1 AC2 6 LYS A 126 GLY A 162 HOH A 405 HOH A 448 SITE 2 AC2 6 HOH A 502 HOH A 625 SITE 1 AC3 2 HOH B 444 HOH B 524 SITE 1 AC4 12 ASP B 102 VAL B 138 ILE B 139 ILE B 140 SITE 2 AC4 12 ILE B 166 THR B 168 SER B 169 THR B 170 SITE 3 AC4 12 MET B 185 LYS B 201 ALA B 203 HOH B 554 CRYST1 61.750 53.870 80.530 90.00 110.68 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 0.016194 0.000000 0.006113 0.00000 SCALE2 0.000000 0.018563 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013273 0.00000