HEADER HYDROLASE 23-AUG-16 5T25 TITLE KINETIC, SPECTRAL AND STRUCTURAL CHARACTERIZATION OF THE SLOW BINDING TITLE 2 INHIBITOR ACETOPYRUVATE WITH DIHYDRODIPICOLINATE SYNTHASE FROM TITLE 3 ESCHERICHIA COLI. COMPND MOL_ID: 1; COMPND 2 MOLECULE: 4-HYDROXY-TETRAHYDRODIPICOLINATE SYNTHASE; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: HTPA SYNTHASE; COMPND 5 EC: 4.3.3.7; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI O8 (STRAIN IAI1); SOURCE 3 ORGANISM_TAXID: 585034; SOURCE 4 STRAIN: IAI1; SOURCE 5 GENE: DAPA, ECIAI1_2529; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS DIHYDRODIPICOLINATE SYNTHASE, KINETICS, ACETOPYRUVATE MODIFICATION, KEYWDS 2 HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR L.CHOOBACK,L.M.THOMAS,W.E.KARSTEN,C.D.FLEMING,P.SEABOURN REVDAT 5 15-NOV-23 5T25 1 LINK REVDAT 4 04-OCT-23 5T25 1 LINK REVDAT 3 07-NOV-18 5T25 1 SOURCE REVDAT 2 17-MAY-17 5T25 1 REMARK HETSYN REVDAT 1 01-MAR-17 5T25 0 JRNL AUTH L.CHOOBACK,L.M.THOMAS,W.E.KARSTEN,C.D.FLEMING,P.SEABOURN JRNL TITL KINETIC, SPECTRAL AND STRUCTURAL CHARACTERIZATION OF THE JRNL TITL 2 SLOW BINDING INHIBITOR ACETOPYRUVATE WITH JRNL TITL 3 DIHYDRODIPICOLINATE SYNTHASE FROM ESCHERICHIA COLI. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.99 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.11.1_2575: ???) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : ML REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 26.81 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.340 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.7 REMARK 3 NUMBER OF REFLECTIONS : 41146 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.161 REMARK 3 R VALUE (WORKING SET) : 0.158 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 2083 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 26.8086 - 4.9020 1.00 2766 142 0.1596 0.1923 REMARK 3 2 4.9020 - 3.8947 0.99 2641 160 0.1329 0.1665 REMARK 3 3 3.8947 - 3.4035 0.99 2666 156 0.1334 0.2053 REMARK 3 4 3.4035 - 3.0928 0.87 2334 116 0.1542 0.1802 REMARK 3 5 3.0928 - 2.8714 0.87 2350 117 0.1626 0.2133 REMARK 3 6 2.8714 - 2.7023 1.00 2646 141 0.1680 0.2677 REMARK 3 7 2.7023 - 2.5671 1.00 2633 146 0.1593 0.2379 REMARK 3 8 2.5671 - 2.4554 1.00 2659 136 0.1649 0.2237 REMARK 3 9 2.4554 - 2.3609 1.00 2685 131 0.1703 0.2088 REMARK 3 10 2.3609 - 2.2795 1.00 2664 135 0.1649 0.2415 REMARK 3 11 2.2795 - 2.2083 1.00 2659 145 0.1663 0.2437 REMARK 3 12 2.2083 - 2.1452 1.00 2621 152 0.1699 0.2152 REMARK 3 13 2.1452 - 2.0887 1.00 2619 134 0.1781 0.2197 REMARK 3 14 2.0887 - 2.0378 1.00 2658 137 0.1834 0.2841 REMARK 3 15 2.0378 - 1.9915 0.94 2462 135 0.2200 0.2738 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) : 0.200 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.090 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 : 0.007 4495 REMARK 3 ANGLE : 0.891 6105 REMARK 3 CHIRALITY : 0.053 735 REMARK 3 PLANARITY : 0.006 794 REMARK 3 DIHEDRAL : 3.555 2731 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 5T25 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-AUG-16. REMARK 100 THE DEPOSITION ID IS D_1000223441. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 10-JUL-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.1 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 : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54178 REMARK 200 MONOCHROMATOR : MULTILAYER OPTICS REMARK 200 OPTICS : VERIMAXHF REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 200K REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 193325 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 81.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 4.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.03 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.54000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.911 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: 1YXC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.45 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 20% PEG3350 200MM SODIUM TARTARATE REMARK 280 14.7 MM HEPES PH 7.1, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE REMARK 280 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z REMARK 290 4555 -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 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 68.32350 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 28.19250 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 68.32350 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 28.19250 REMARK 290 SMTRY3 4 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4040 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20790 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -116.0 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 HIS B 0 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 612 O HOH A 657 2.04 REMARK 500 NH1 ARG A 279 O HOH A 401 2.06 REMARK 500 NH1 ARG B 283 O HOH B 401 2.11 REMARK 500 NH1 ARG B 279 O HOH B 402 2.12 REMARK 500 O HOH A 488 O HOH A 626 2.15 REMARK 500 NH1 ARG B 230 O HOH B 403 2.15 REMARK 500 O HOH B 649 O HOH B 678 2.15 REMARK 500 O HOH B 505 O HOH B 659 2.15 REMARK 500 O HOH A 564 O HOH A 670 2.15 REMARK 500 O HOH A 546 O HOH A 613 2.16 REMARK 500 OD2 ASP B 94 O HOH B 404 2.16 REMARK 500 O HOH A 503 O HOH A 667 2.16 REMARK 500 O HOH B 610 O HOH B 654 2.17 REMARK 500 O HOH B 586 O HOH B 681 2.18 REMARK 500 O HOH A 583 O HOH A 589 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 679 O HOH B 663 2656 2.16 REMARK 500 O HOH A 684 O HOH B 662 2656 2.17 REMARK 500 O HOH A 638 O HOH B 697 4545 2.18 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 CYS A 141 CB CYS A 141 SG -0.111 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 PHE A 2 49.06 -98.12 REMARK 500 TYR A 107 -43.42 77.22 REMARK 500 PRO A 249 30.15 -99.58 REMARK 500 TYR B 107 -39.53 79.98 REMARK 500 VAL B 135 75.14 -150.18 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 B 734 DISTANCE = 5.82 ANGSTROMS REMARK 525 HOH B 735 DISTANCE = 5.90 ANGSTROMS REMARK 525 HOH B 736 DISTANCE = 5.93 ANGSTROMS REMARK 525 HOH B 737 DISTANCE = 6.07 ANGSTROMS REMARK 525 HOH B 738 DISTANCE = 6.16 ANGSTROMS REMARK 525 HOH B 739 DISTANCE = 6.38 ANGSTROMS REMARK 525 HOH B 740 DISTANCE = 6.55 ANGSTROMS REMARK 525 HOH B 741 DISTANCE = 7.10 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 NA A 303 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 THR A 77 OG1 REMARK 620 2 THR A 89 OG1 101.9 REMARK 620 3 GLN A 130 OE1 128.6 125.7 REMARK 620 4 HOH A 452 O 79.5 83.4 120.1 REMARK 620 N 1 2 3 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 304 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA A 152 O REMARK 620 2 VAL A 154 O 82.4 REMARK 620 3 LYS A 155 O 151.2 73.0 REMARK 620 4 ILE A 157 O 92.7 76.6 95.8 REMARK 620 5 HOH A 403 O 65.3 103.8 105.9 157.5 REMARK 620 6 HOH A 611 O 78.6 153.0 129.4 85.3 85.4 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 302 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 SER A 185 OG REMARK 620 2 SER A 190 OG 121.0 REMARK 620 3 HOH A 518 O 109.6 99.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 305 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 265 OD2 REMARK 620 2 HOH A 507 O 84.9 REMARK 620 3 HOH A 627 O 99.3 106.6 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA A 306 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH A 692 O REMARK 620 2 HOH A 711 O 77.4 REMARK 620 N 1 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 305 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 PRO B 110 O REMARK 620 2 HOH B 540 O 113.6 REMARK 620 3 HOH B 707 O 103.3 99.9 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 302 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ALA B 152 O REMARK 620 2 VAL B 154 O 78.6 REMARK 620 3 LYS B 155 O 136.2 62.0 REMARK 620 4 ILE B 157 O 91.7 82.1 100.3 REMARK 620 5 HOH B 652 O 83.9 161.0 137.0 91.1 REMARK 620 6 HOH B 671 O 80.4 80.2 75.2 161.8 104.2 REMARK 620 N 1 2 3 4 5 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA B 304 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HOH B 594 O REMARK 620 2 HOH B 683 O 122.4 REMARK 620 3 HOH B 711 O 119.0 103.0 REMARK 620 N 1 2 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LYS A 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC5 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC6 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA A 306 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC7 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue LYS B 301 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC8 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 302 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC9 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 303 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 304 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 305 REMARK 800 REMARK 800 SITE_IDENTIFIER: AD3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue NA B 306 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5T26 RELATED DB: PDB DBREF 5T25 A 1 291 UNP B7M7I1 DAPA_ECO8A 1 292 DBREF 5T25 B 1 292 UNP B7M7I1 DAPA_ECO8A 1 292 SEQADV 5T25 HIS A 0 UNP B7M7I1 EXPRESSION TAG SEQADV 5T25 HIS B 0 UNP B7M7I1 EXPRESSION TAG SEQRES 1 A 293 HIS MET PHE THR GLY SER ILE VAL ALA ILE VAL THR PRO SEQRES 2 A 293 MET ASP GLU LYS GLY ASN VAL CYS ARG ALA SER LEU LYS SEQRES 3 A 293 LYS LEU ILE ASP TYR HIS VAL ALA SER GLY THR SER ALA SEQRES 4 A 293 ILE VAL SER VAL GLY THR THR GLY GLU SER ALA THR LEU SEQRES 5 A 293 ASN HIS ASP GLU HIS ALA ASP VAL VAL MET MET THR LEU SEQRES 6 A 293 ASP LEU ALA ASP GLY ARG ILE PRO VAL ILE ALA GLY THR SEQRES 7 A 293 GLY ALA ASN ALA THR ALA GLU ALA ILE SER LEU THR GLN SEQRES 8 A 293 ARG PHE ASN ASP SER GLY ILE VAL GLY CYS LEU THR VAL SEQRES 9 A 293 THR PRO TYR TYR ASN ARG PRO SER GLN GLU GLY LEU TYR SEQRES 10 A 293 GLN HIS PHE LYS ALA ILE ALA GLU HIS THR ASP LEU PRO SEQRES 11 A 293 GLN ILE LEU TYR ASN VAL PRO SER ARG THR GLY CYS ASP SEQRES 12 A 293 LEU LEU PRO GLU THR VAL GLY ARG LEU ALA LYS VAL LYS SEQRES 13 A 293 ASN ILE ILE GLY ILE 74P GLU ALA THR GLY ASN LEU THR SEQRES 14 A 293 ARG VAL ASN GLN ILE LYS GLU LEU VAL SER ASP ASP PHE SEQRES 15 A 293 VAL LEU LEU SER GLY ASP ASP ALA SER ALA LEU ASP PHE SEQRES 16 A 293 MET GLN LEU GLY GLY HIS GLY VAL ILE SER VAL THR ALA SEQRES 17 A 293 ASN VAL ALA ALA ARG ASP MET ALA GLN MET CYS LYS LEU SEQRES 18 A 293 ALA ALA GLU GLY HIS PHE ALA GLU ALA ARG VAL ILE ASN SEQRES 19 A 293 GLN ARG LEU MET PRO LEU HIS ASN LYS LEU PHE VAL GLU SEQRES 20 A 293 PRO ASN PRO ILE PRO VAL LYS TRP ALA CYS LYS GLU LEU SEQRES 21 A 293 GLY LEU VAL ALA THR ASP THR LEU ARG LEU PRO MET THR SEQRES 22 A 293 PRO ILE THR ASP SER GLY ARG GLU THR VAL ARG ALA ALA SEQRES 23 A 293 LEU LYS HIS ALA GLY LEU LEU SEQRES 1 B 293 HIS MET PHE THR GLY SER ILE VAL ALA ILE VAL THR PRO SEQRES 2 B 293 MET ASP GLU LYS GLY ASN VAL CYS ARG ALA SER LEU LYS SEQRES 3 B 293 LYS LEU ILE ASP TYR HIS VAL ALA SER GLY THR SER ALA SEQRES 4 B 293 ILE VAL SER VAL GLY THR THR GLY GLU SER ALA THR LEU SEQRES 5 B 293 ASN HIS ASP GLU HIS ALA ASP VAL VAL MET MET THR LEU SEQRES 6 B 293 ASP LEU ALA ASP GLY ARG ILE PRO VAL ILE ALA GLY THR SEQRES 7 B 293 GLY ALA ASN ALA THR ALA GLU ALA ILE SER LEU THR GLN SEQRES 8 B 293 ARG PHE ASN ASP SER GLY ILE VAL GLY CYS LEU THR VAL SEQRES 9 B 293 THR PRO TYR TYR ASN ARG PRO SER GLN GLU GLY LEU TYR SEQRES 10 B 293 GLN HIS PHE LYS ALA ILE ALA GLU HIS THR ASP LEU PRO SEQRES 11 B 293 GLN ILE LEU TYR ASN VAL PRO SER ARG THR GLY CYS ASP SEQRES 12 B 293 LEU LEU PRO GLU THR VAL GLY ARG LEU ALA LYS VAL LYS SEQRES 13 B 293 ASN ILE ILE GLY ILE 74P GLU ALA THR GLY ASN LEU THR SEQRES 14 B 293 ARG VAL ASN GLN ILE LYS GLU LEU VAL SER ASP ASP PHE SEQRES 15 B 293 VAL LEU LEU SER GLY ASP ASP ALA SER ALA LEU ASP PHE SEQRES 16 B 293 MET GLN LEU GLY GLY HIS GLY VAL ILE SER VAL THR ALA SEQRES 17 B 293 ASN VAL ALA ALA ARG ASP MET ALA GLN MET CYS LYS LEU SEQRES 18 B 293 ALA ALA GLU GLY HIS PHE ALA GLU ALA ARG VAL ILE ASN SEQRES 19 B 293 GLN ARG LEU MET PRO LEU HIS ASN LYS LEU PHE VAL GLU SEQRES 20 B 293 PRO ASN PRO ILE PRO VAL LYS TRP ALA CYS LYS GLU LEU SEQRES 21 B 293 GLY LEU VAL ALA THR ASP THR LEU ARG LEU PRO MET THR SEQRES 22 B 293 PRO ILE THR ASP SER GLY ARG GLU THR VAL ARG ALA ALA SEQRES 23 B 293 LEU LYS HIS ALA GLY LEU LEU MODRES 5T25 74P B 161 LYS MODIFIED RESIDUE HET 74P A 161 17 HET 74P B 161 17 HET LYS A 301 10 HET NA A 302 1 HET NA A 303 1 HET NA A 304 1 HET NA A 305 1 HET NA A 306 1 HET LYS B 301 10 HET NA B 302 1 HET NA B 303 1 HET NA B 304 1 HET NA B 305 1 HET NA B 306 1 HETNAM 74P (E)-N~6~-(1-CARBOXY-3-OXOBUTYLIDENE)-L-LYSINE HETNAM LYS LYSINE HETNAM NA SODIUM ION FORMUL 1 74P 2(C11 H18 N2 O5) FORMUL 3 LYS 2(C6 H15 N2 O2 1+) FORMUL 4 NA 10(NA 1+) FORMUL 15 HOH *660(H2 O) HELIX 1 AA1 CYS A 20 GLY A 35 1 16 HELIX 2 AA2 GLU A 47 LEU A 51 5 5 HELIX 3 AA3 ASN A 52 ASP A 68 1 17 HELIX 4 AA4 ALA A 81 ASN A 93 1 13 HELIX 5 AA5 SER A 111 GLU A 124 1 14 HELIX 6 AA6 VAL A 135 GLY A 140 1 6 HELIX 7 AA7 LEU A 144 LYS A 153 1 10 HELIX 8 AA8 THR A 168 GLU A 175 1 8 HELIX 9 AA9 ASP A 187 ALA A 189 5 3 HELIX 10 AB1 SER A 190 LEU A 197 1 8 HELIX 11 AB2 VAL A 205 VAL A 209 5 5 HELIX 12 AB3 ALA A 210 GLU A 223 1 14 HELIX 13 AB4 HIS A 225 LEU A 243 1 19 HELIX 14 AB5 PRO A 249 LEU A 259 1 11 HELIX 15 AB6 THR A 275 ALA A 289 1 15 HELIX 16 AB7 CYS B 20 GLY B 35 1 16 HELIX 17 AB8 GLU B 47 LEU B 51 5 5 HELIX 18 AB9 ASN B 52 ASP B 68 1 17 HELIX 19 AC1 ALA B 81 PHE B 92 1 12 HELIX 20 AC2 SER B 111 GLU B 124 1 14 HELIX 21 AC3 VAL B 135 GLY B 140 1 6 HELIX 22 AC4 LEU B 144 LYS B 153 1 10 HELIX 23 AC5 THR B 168 GLU B 175 1 8 HELIX 24 AC6 ASP B 187 ALA B 189 5 3 HELIX 25 AC7 SER B 190 LEU B 197 1 8 HELIX 26 AC8 VAL B 205 VAL B 209 5 5 HELIX 27 AC9 ALA B 210 GLU B 223 1 14 HELIX 28 AD1 HIS B 225 LEU B 243 1 19 HELIX 29 AD2 PRO B 249 LEU B 259 1 11 HELIX 30 AD3 THR B 275 ALA B 289 1 15 SHEET 1 AA1 9 GLY A 4 ALA A 8 0 SHEET 2 AA1 9 ALA A 38 SER A 41 1 O VAL A 40 N VAL A 7 SHEET 3 AA1 9 VAL A 73 GLY A 76 1 O ILE A 74 N ILE A 39 SHEET 4 AA1 9 GLY A 99 VAL A 103 1 O LEU A 101 N ALA A 75 SHEET 5 AA1 9 GLN A 130 ASN A 134 1 O ILE A 131 N CYS A 100 SHEET 6 AA1 9 ILE A 157 GLU A 162 1 O 74P A 161 N LEU A 132 SHEET 7 AA1 9 VAL A 182 SER A 185 1 O VAL A 182 N ILE A 158 SHEET 8 AA1 9 GLY A 201 SER A 204 1 O ILE A 203 N SER A 185 SHEET 9 AA1 9 GLY A 4 ALA A 8 1 N ILE A 6 O SER A 204 SHEET 1 AA2 9 GLY B 4 ALA B 8 0 SHEET 2 AA2 9 ALA B 38 SER B 41 1 O VAL B 40 N VAL B 7 SHEET 3 AA2 9 VAL B 73 GLY B 76 1 O ILE B 74 N ILE B 39 SHEET 4 AA2 9 GLY B 99 VAL B 103 1 O LEU B 101 N ALA B 75 SHEET 5 AA2 9 GLN B 130 ASN B 134 1 O ILE B 131 N CYS B 100 SHEET 6 AA2 9 ILE B 157 GLU B 162 1 O 74P B 161 N LEU B 132 SHEET 7 AA2 9 VAL B 182 SER B 185 1 O LEU B 184 N GLU B 162 SHEET 8 AA2 9 GLY B 201 SER B 204 1 O ILE B 203 N SER B 185 SHEET 9 AA2 9 GLY B 4 ALA B 8 1 N ILE B 6 O SER B 204 LINK C ILE A 160 N 74P A 161 1555 1555 1.33 LINK C 74P A 161 N GLU A 162 1555 1555 1.33 LINK C ILE B 160 N 74P B 161 1555 1555 1.32 LINK C 74P B 161 N GLU B 162 1555 1555 1.32 LINK OG1 THR A 77 NA NA A 303 1555 1555 2.60 LINK OG1 THR A 89 NA NA A 303 1555 1555 2.67 LINK OE1 GLN A 130 NA NA A 303 1555 1555 2.72 LINK O ALA A 152 NA NA A 304 1555 1555 2.74 LINK O VAL A 154 NA NA A 304 1555 1555 2.89 LINK O LYS A 155 NA NA A 304 1555 1555 2.95 LINK O ILE A 157 NA NA A 304 1555 1555 2.73 LINK OG SER A 185 NA NA A 302 1555 1555 2.50 LINK OG SER A 190 NA NA A 302 1555 1555 2.72 LINK OD2 ASP A 265 NA NA A 305 1555 1555 2.97 LINK NA NA A 302 O HOH A 518 1555 1555 2.81 LINK NA NA A 303 O HOH A 452 1555 1555 2.67 LINK NA NA A 304 O HOH A 403 1555 1555 2.96 LINK NA NA A 304 O HOH A 611 1555 1555 2.29 LINK NA NA A 305 O HOH A 507 1555 1555 2.52 LINK NA NA A 305 O HOH A 627 1555 1555 3.03 LINK NA NA A 306 O HOH A 692 1555 1555 2.87 LINK NA NA A 306 O HOH A 711 1555 1555 2.96 LINK O PRO B 110 NA NA B 305 1555 1555 2.83 LINK O ALA B 152 NA NA B 302 1555 1555 2.79 LINK O VAL B 154 NA NA B 302 1555 1555 2.91 LINK O LYS B 155 NA NA B 302 1555 1555 3.11 LINK O ILE B 157 NA NA B 302 1555 1555 2.65 LINK NA NA B 302 O HOH B 652 1555 1555 2.39 LINK NA NA B 302 O HOH B 671 1555 1555 2.98 LINK NA NA B 303 O HOH B 416 1555 1555 3.10 LINK NA NA B 304 O HOH B 594 1555 1555 3.10 LINK NA NA B 304 O HOH B 683 1555 1555 2.83 LINK NA NA B 304 O HOH B 711 1555 1555 2.51 LINK NA NA B 305 O HOH B 540 1555 1555 2.90 LINK NA NA B 305 O HOH B 707 1555 1555 2.59 LINK NA NA B 306 O HOH B 689 1555 1555 3.18 CISPEP 1 ASN A 248 PRO A 249 0 8.90 CISPEP 2 LEU A 269 PRO A 270 0 14.82 CISPEP 3 ASN B 248 PRO B 249 0 11.86 CISPEP 4 LEU B 269 PRO B 270 0 13.26 SITE 1 AC1 11 SER A 48 ALA A 49 LEU A 51 HIS A 53 SITE 2 AC1 11 HIS A 56 TYR A 106 HOH A 433 HOH A 556 SITE 3 AC1 11 HOH A 561 ASN B 80 GLU B 84 SITE 1 AC2 5 SER A 185 ASP A 187 SER A 190 PHE A 194 SITE 2 AC2 5 HOH A 518 SITE 1 AC3 6 THR A 77 THR A 89 CYS A 100 ILE A 122 SITE 2 AC3 6 GLN A 130 HOH A 452 SITE 1 AC4 6 ALA A 152 VAL A 154 LYS A 155 ILE A 157 SITE 2 AC4 6 HOH A 403 HOH A 611 SITE 1 AC5 5 ASP A 265 PRO A 273 ILE A 274 HOH A 507 SITE 2 AC5 5 HOH A 627 SITE 1 AC6 4 ARG A 21 ALA A 22 HOH A 692 HOH A 711 SITE 1 AC7 10 ASN A 80 GLU A 84 SER B 48 ALA B 49 SITE 2 AC7 10 LEU B 51 HIS B 56 TYR B 106 HOH B 409 SITE 3 AC7 10 HOH B 549 HOH B 577 SITE 1 AC8 6 ALA B 152 VAL B 154 LYS B 155 ILE B 157 SITE 2 AC8 6 HOH B 652 HOH B 671 SITE 1 AC9 3 LEU B 144 PRO B 145 GLU B 146 SITE 1 AD1 6 SER B 111 GLN B 112 GLU B 113 HOH B 594 SITE 2 AD1 6 HOH B 683 HOH B 711 SITE 1 AD2 5 PRO B 110 SER B 111 GLN B 112 HOH B 540 SITE 2 AD2 5 HOH B 707 SITE 1 AD3 2 ARG B 21 ALA B 22 CRYST1 136.647 56.385 101.530 90.00 127.62 90.00 C 1 2 1 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 0.007318 0.000000 0.005640 0.00000 SCALE2 0.000000 0.017735 0.000000 0.00000 SCALE3 0.000000 0.000000 0.012435 0.00000