HEADER LYASE 04-JUN-20 6Z9I TITLE ESCHERICHIA COLI D-2-DEOXYRIBOSE-5-PHOSPHATE ALDOLASE - N21K MUTANT TITLE 2 COMPLEX WITH REACTION PRODUCTS 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 6Z9I 1 REMARK REVDAT 2 25-NOV-20 6Z9I 1 JRNL REVDAT 1 18-NOV-20 6Z9I 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. 1.86 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) : 1.86 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 19.27 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 3 NUMBER OF REFLECTIONS : 39732 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.164 REMARK 3 R VALUE (WORKING SET) : 0.161 REMARK 3 FREE R VALUE : 0.209 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1986 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 19.2700 - 4.4700 0.99 2900 150 0.1284 0.1587 REMARK 3 2 4.4700 - 3.5500 0.98 2832 148 0.1173 0.1456 REMARK 3 3 3.5500 - 3.1100 0.97 2767 147 0.1431 0.2005 REMARK 3 4 3.1100 - 2.8200 0.98 2770 145 0.1596 0.2167 REMARK 3 5 2.8200 - 2.6200 0.97 2743 149 0.1626 0.2009 REMARK 3 6 2.6200 - 2.4700 0.95 2710 143 0.1808 0.2284 REMARK 3 7 2.4700 - 2.3400 0.96 2733 138 0.1698 0.2212 REMARK 3 8 2.3400 - 2.2400 0.95 2668 145 0.1750 0.2420 REMARK 3 9 2.2400 - 2.1600 0.95 2660 136 0.1650 0.2134 REMARK 3 10 2.1600 - 2.0800 0.94 2664 137 0.1787 0.2309 REMARK 3 11 2.0800 - 2.0200 0.94 2656 148 0.1848 0.2522 REMARK 3 12 2.0200 - 1.9600 0.94 2653 141 0.2023 0.2468 REMARK 3 13 1.9600 - 1.9100 0.93 2597 134 0.2280 0.3088 REMARK 3 14 1.9100 - 1.8600 0.84 2393 125 0.2900 0.3594 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) : 0.208 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 21.383 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 14.88 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.14 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 : 0.006 3910 REMARK 3 ANGLE : 0.792 5305 REMARK 3 CHIRALITY : 0.050 625 REMARK 3 PLANARITY : 0.005 692 REMARK 3 DIHEDRAL : 12.483 2417 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 6Z9I COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-JUN-20. REMARK 100 THE DEPOSITION ID IS D_1292108812. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 23-MAR-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS FR591 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MAR SCANNER 345 MM PLATE REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS NOV 1, 2016 REMARK 200 DATA SCALING SOFTWARE : XDS NOV 1, 2016 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39746 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.860 REMARK 200 RESOLUTION RANGE LOW (A) : 19.270 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.9 REMARK 200 DATA REDUNDANCY : 3.570 REMARK 200 R MERGE (I) : 0.10600 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.86 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 90.2 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.55000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.300 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 (%): 47.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, MAGNESIUM FORMATE, TRIS, PH REMARK 280 8.0, 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 26.65000 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 1 REMARK 465 THR A 2 REMARK 465 MET B 1 REMARK 465 THR B 2 REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLU B 27 CD OE1 OE2 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT REMARK 500 REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT. REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI DISTANCE REMARK 500 O HOH A 594 O HOH A 620 2.08 REMARK 500 O HOH B 672 O HOH B 700 2.08 REMARK 500 O HOH B 420 O HOH B 638 2.12 REMARK 500 OD2 ASP A 147 O HOH A 401 2.13 REMARK 500 OD2 ASP B 211 O HOH B 401 2.14 REMARK 500 O HOH A 670 O HOH A 762 2.14 REMARK 500 O HOH A 477 O HOH A 735 2.15 REMARK 500 O HOH A 420 O HOH B 646 2.15 REMARK 500 O HOH A 433 O HOH A 553 2.16 REMARK 500 O HOH B 416 O HOH B 697 2.16 REMARK 500 O HOH A 624 O HOH A 755 2.17 REMARK 500 OE2 GLU A 156 O HOH A 402 2.18 REMARK 500 O HOH A 622 O HOH B 567 2.18 REMARK 500 O HOH A 604 O HOH A 678 2.19 REMARK 500 O HOH B 737 O HOH B 781 2.19 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 A 530 O HOH A 596 2454 2.03 REMARK 500 O HOH A 607 O HOH A 641 2454 2.08 REMARK 500 NZ LYS A 214 OE1 GLU B 62 2454 2.10 REMARK 500 O HOH B 408 O HOH B 635 2545 2.17 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 63.13 62.13 REMARK 500 LYS A 146 -57.90 72.73 REMARK 500 ASN A 176 -133.46 -120.58 REMARK 500 SER A 238 -78.87 -129.54 REMARK 500 GLU B 141 65.77 63.01 REMARK 500 LYS B 146 -60.03 69.04 REMARK 500 LYS B 146 -58.70 69.04 REMARK 500 ASN B 176 -134.59 -126.81 REMARK 500 SER B 239 40.38 -149.25 REMARK 500 SER B 239 40.63 -149.38 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 777 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH A 778 DISTANCE = 7.46 ANGSTROMS REMARK 525 HOH A 779 DISTANCE = 11.96 ANGSTROMS REMARK 525 HOH B 785 DISTANCE = 5.92 ANGSTROMS REMARK 525 HOH B 786 DISTANCE = 6.74 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 A 303 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 81 OD2 REMARK 620 2 HOH A 421 O 83.7 REMARK 620 3 HOH A 447 O 89.4 81.4 REMARK 620 4 HOH A 570 O 80.3 162.3 90.9 REMARK 620 5 HOH A 611 O 97.6 94.8 171.7 94.8 REMARK 620 6 HOH A 654 O 162.2 78.5 88.3 117.4 83.7 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 MG A 302 MG REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 418 O REMARK 620 2 HOH A 478 O 91.6 REMARK 620 3 HOH A 538 O 87.0 86.9 REMARK 620 4 HOH A 682 O 78.2 89.8 164.7 REMARK 620 5 HOH A 750 O 72.3 163.2 87.1 91.9 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 MG A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue MG A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue G3H B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 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 6Z9I A 1 250 UNP E2QLE1 E2QLE1_ECOLX 1 250 DBREF 6Z9I B 1 250 UNP E2QLE1 E2QLE1_ECOLX 1 250 SEQADV 6Z9I LYS A 21 UNP E2QLE1 ASN 21 ENGINEERED MUTATION SEQADV 6Z9I LYS B 21 UNP E2QLE1 ASN 21 ENGINEERED MUTATION SEQRES 1 A 250 MET THR ASP LEU LYS ALA SER SER LEU ARG ALA LEU LYS SEQRES 2 A 250 LEU MET ASP LEU THR THR LEU LYS ASP ASP ASP THR ASP SEQRES 3 A 250 GLU LYS VAL ILE ALA LEU CYS HIS GLN ALA LYS THR PRO SEQRES 4 A 250 VAL GLY ASN THR ALA ALA ILE CYS ILE TYR PRO ARG PHE SEQRES 5 A 250 ILE PRO ILE ALA ARG LYS THR LEU LYS GLU GLN GLY THR SEQRES 6 A 250 PRO GLU ILE ARG ILE ALA THR VAL THR ASN PHE PRO HIS SEQRES 7 A 250 GLY ASN ASP ASP ILE ASP ILE ALA LEU ALA GLU THR ARG SEQRES 8 A 250 ALA ALA ILE ALA TYR GLY ALA ASP GLU VAL ASP VAL VAL SEQRES 9 A 250 PHE PRO TYR ARG ALA LEU MET ALA GLY ASN GLU GLN VAL SEQRES 10 A 250 GLY PHE ASP LEU VAL LYS ALA CYS LYS GLU ALA CYS ALA SEQRES 11 A 250 ALA ALA ASN VAL LEU LEU LYS VAL ILE ILE GLU THR GLY SEQRES 12 A 250 GLU LEU LYS ASP GLU ALA LEU ILE ARG LYS ALA SER GLU SEQRES 13 A 250 ILE SER ILE LYS ALA GLY ALA ASP PHE ILE LYS THR SER SEQRES 14 A 250 THR GLY LYS VAL ALA VAL ASN ALA THR PRO GLU SER ALA SEQRES 15 A 250 ARG ILE MET MET GLU VAL ILE ARG ASP MET GLY VAL GLU SEQRES 16 A 250 LYS THR VAL GLY PHE LYS PRO ALA GLY GLY VAL ARG THR SEQRES 17 A 250 ALA GLU ASP ALA GLN LYS TYR LEU ALA ILE ALA ASP GLU SEQRES 18 A 250 LEU PHE GLY ALA ASP TRP ALA ASP ALA ARG HIS TYR ARG SEQRES 19 A 250 PHE GLY ALA SER SER LEU LEU ALA SER LEU LEU LYS ALA SEQRES 20 A 250 LEU GLY HIS SEQRES 1 B 250 MET THR ASP LEU LYS ALA SER SER LEU ARG ALA LEU LYS SEQRES 2 B 250 LEU MET ASP LEU THR THR LEU LYS ASP ASP ASP THR ASP SEQRES 3 B 250 GLU LYS VAL ILE ALA LEU CYS HIS GLN ALA LYS THR PRO SEQRES 4 B 250 VAL GLY ASN THR ALA ALA ILE CYS ILE TYR PRO ARG PHE SEQRES 5 B 250 ILE PRO ILE ALA ARG LYS THR LEU LYS GLU GLN GLY THR SEQRES 6 B 250 PRO GLU ILE ARG ILE ALA THR VAL THR ASN PHE PRO HIS SEQRES 7 B 250 GLY ASN ASP ASP ILE ASP ILE ALA LEU ALA GLU THR ARG SEQRES 8 B 250 ALA ALA ILE ALA TYR GLY ALA ASP GLU VAL ASP VAL VAL SEQRES 9 B 250 PHE PRO TYR ARG ALA LEU MET ALA GLY ASN GLU GLN VAL SEQRES 10 B 250 GLY PHE ASP LEU VAL LYS ALA CYS LYS GLU ALA CYS ALA SEQRES 11 B 250 ALA ALA ASN VAL LEU LEU LYS VAL ILE ILE GLU THR GLY SEQRES 12 B 250 GLU LEU LYS ASP GLU ALA LEU ILE ARG LYS ALA SER GLU SEQRES 13 B 250 ILE SER ILE LYS ALA GLY ALA ASP PHE ILE LYS THR SER SEQRES 14 B 250 THR GLY LYS VAL ALA VAL ASN ALA THR PRO GLU SER ALA SEQRES 15 B 250 ARG ILE MET MET GLU VAL ILE ARG ASP MET GLY VAL GLU SEQRES 16 B 250 LYS THR VAL GLY PHE LYS PRO ALA GLY GLY VAL ARG THR SEQRES 17 B 250 ALA GLU ASP ALA GLN LYS TYR LEU ALA ILE ALA ASP GLU SEQRES 18 B 250 LEU PHE GLY ALA ASP TRP ALA ASP ALA ARG HIS TYR ARG SEQRES 19 B 250 PHE GLY ALA SER SER LEU LEU ALA SER LEU LEU LYS ALA SEQRES 20 B 250 LEU GLY HIS HET EDO A 301 2 HET MG A 302 1 HET MG A 303 1 HET EDO B 301 2 HET G3H B 302 10 HETNAM EDO 1,2-ETHANEDIOL HETNAM MG MAGNESIUM ION HETNAM G3H GLYCERALDEHYDE-3-PHOSPHATE HETSYN EDO ETHYLENE GLYCOL FORMUL 3 EDO 2(C2 H6 O2) FORMUL 4 MG 2(MG 2+) FORMUL 7 G3H C3 H7 O6 P FORMUL 8 HOH *765(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 SER A 239 GLY A 249 1 11 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 103 O ILE A 139 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 CYS A 47 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 ALA A 45 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 ILE B 48 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 ALA B 45 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 1.33 LINK OD2 ASP A 81 MG MG A 303 1555 1555 2.05 LINK MG MG A 302 O HOH A 418 1555 1555 2.54 LINK MG MG A 302 O HOH A 478 1555 2444 2.39 LINK MG MG A 302 O HOH A 538 1555 2444 2.25 LINK MG MG A 302 O HOH A 682 1555 1555 2.00 LINK MG MG A 302 O HOH A 750 1555 1555 2.29 LINK MG MG A 303 O HOH A 421 1555 1555 2.32 LINK MG MG A 303 O HOH A 447 1555 2444 2.24 LINK MG MG A 303 O HOH A 570 1555 1555 2.45 LINK MG MG A 303 O HOH A 611 1555 1555 2.12 LINK MG MG A 303 O HOH A 654 1555 2444 2.10 CISPEP 1 PHE A 76 PRO A 77 0 0.13 CISPEP 2 PHE B 76 PRO B 77 0 -1.85 SITE 1 AC1 4 LYS A 167 SER A 169 THR A 170 HOH A 554 SITE 1 AC2 3 HOH A 418 HOH A 682 HOH A 750 SITE 1 AC3 4 ASP A 81 HOH A 421 HOH A 570 HOH A 611 SITE 1 AC4 15 THR B 18 LYS B 167 THR B 170 GLY B 204 SITE 2 AC4 15 GLY B 205 ARG B 207 GLY B 236 ALA B 237 SITE 3 AC4 15 SER B 238 EDO B 301 HOH B 402 HOH B 407 SITE 4 AC4 15 HOH B 465 HOH B 513 HOH B 572 SITE 1 AC5 13 VAL B 73 PHE B 76 ASP B 102 VAL B 138 SITE 2 AC5 13 ILE B 139 ILE B 140 ILE B 166 THR B 168 SITE 3 AC5 13 SER B 169 THR B 170 LYS B 201 ALA B 203 SITE 4 AC5 13 G3H B 302 CRYST1 61.900 53.300 81.200 90.00 110.20 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 0.016155 0.000000 0.005944 0.00000 SCALE2 0.000000 0.018762 0.000000 0.00000 SCALE3 0.000000 0.000000 0.013122 0.00000