HEADER HYDROLASE 01-MAY-17 5VO3 TITLE CRYSTAL STRUCTURE OF DAPE IN COMPLEX WITH THE PRODUCTS (SUCCINIC ACID TITLE 2 AND DIAMINOPIMELIC ACID) COMPND MOL_ID: 1; COMPND 2 MOLECULE: SUCCINYL-DIAMINOPIMELATE DESUCCINYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: SDAP DESUCCINYLASE,N-SUCCINYL-LL-2,6-DIAMINOHEPTANEDIOATE COMPND 5 AMIDOHYDROLASE; COMPND 6 EC: 3.5.1.18; COMPND 7 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HAEMOPHILUS INFLUENZAE; SOURCE 3 ORGANISM_TAXID: 727; SOURCE 4 GENE: DAPE, HI_0102; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 866768 KEYWDS DAPE, HYDROLAZE, SUCCINIC ACID, DIAMINOPIMELIC ACID, M28, STRUCTURAL KEYWDS 2 GENOMICS, PSI-BIOLOGY, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR B.NOCEK REVDAT 3 15-NOV-23 5VO3 1 ATOM REVDAT 2 04-OCT-23 5VO3 1 LINK REVDAT 1 25-JUL-18 5VO3 0 JRNL AUTH B.NOCEK,C.REIDL,A.STARUS,T.HEATH,D.BIENVENUE,J.OSIPIUK, JRNL AUTH 2 R.JEDRZEJCZAK,A.JOACHIMIAK,D.P.BECKER,R.C.HOLZ JRNL TITL STRUCTURAL EVIDENCE OF A MAJOR CONFORMATIONAL CHANGE JRNL TITL 2 TRIGGERED BY SUBSTRATE BINDING IN DAPE ENZYMES: IMPACT ON JRNL TITL 3 THE CATALYTIC MECHANISM. JRNL REF BIOCHEMISTRY V. 57 574 2018 JRNL REFN ISSN 1520-4995 JRNL PMID 29272107 JRNL DOI 10.1021/ACS.BIOCHEM.7B01151 REMARK 2 REMARK 2 RESOLUTION. 1.95 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX DEV_1888 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) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.32 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 73.4 REMARK 3 NUMBER OF REFLECTIONS : 59180 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.163 REMARK 3 R VALUE (WORKING SET) : 0.162 REMARK 3 FREE R VALUE : 0.185 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.110 REMARK 3 FREE R VALUE TEST SET COUNT : 3023 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 35.3268 - 5.4684 0.96 3363 193 0.1752 0.1680 REMARK 3 2 5.4684 - 4.3430 1.00 3484 156 0.1256 0.1522 REMARK 3 3 4.3430 - 3.7947 0.98 3411 202 0.1300 0.1584 REMARK 3 4 3.7947 - 3.4481 0.99 3494 167 0.1540 0.1870 REMARK 3 5 3.4481 - 3.2011 0.99 3415 206 0.1639 0.2129 REMARK 3 6 3.2011 - 3.0125 0.97 3352 178 0.1718 0.2280 REMARK 3 7 3.0125 - 2.8617 0.93 3258 189 0.1730 0.1861 REMARK 3 8 2.8617 - 2.7372 0.87 3007 191 0.1777 0.1637 REMARK 3 9 2.7372 - 2.6318 0.81 2825 153 0.1707 0.2050 REMARK 3 10 2.6318 - 2.5410 0.75 2606 136 0.1786 0.1888 REMARK 3 11 2.5410 - 2.4616 0.73 2526 136 0.1683 0.1652 REMARK 3 12 2.4616 - 2.3913 0.70 2477 128 0.1837 0.2013 REMARK 3 13 2.3913 - 2.3283 0.68 2350 127 0.1868 0.1992 REMARK 3 14 2.3283 - 2.2715 0.67 2324 124 0.1809 0.2053 REMARK 3 15 2.2715 - 2.2199 0.65 2276 129 0.1825 0.1997 REMARK 3 16 2.2199 - 2.1727 0.63 2202 117 0.1857 0.1870 REMARK 3 17 2.1727 - 2.1292 0.59 2074 78 0.1745 0.1902 REMARK 3 18 2.1292 - 2.0890 0.54 1904 88 0.1794 0.2185 REMARK 3 19 2.0890 - 2.0517 0.48 1677 81 0.1791 0.2054 REMARK 3 20 2.0517 - 2.0170 0.44 1487 92 0.1831 0.2269 REMARK 3 21 2.0170 - 1.9844 0.40 1413 76 0.1734 0.2275 REMARK 3 22 1.9844 - 1.9539 0.36 1232 76 0.1807 0.1799 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) : 0.140 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.350 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 : 0.008 3019 REMARK 3 ANGLE : 1.174 4105 REMARK 3 CHIRALITY : 0.115 467 REMARK 3 PLANARITY : 0.005 537 REMARK 3 DIHEDRAL : 13.925 1110 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -3 THROUGH 172 ) REMARK 3 ORIGIN FOR THE GROUP (A): -16.3858 10.8101 30.9508 REMARK 3 T TENSOR REMARK 3 T11: 0.2379 T22: 0.0544 REMARK 3 T33: 0.2508 T12: -0.0395 REMARK 3 T13: 0.0544 T23: -0.0906 REMARK 3 L TENSOR REMARK 3 L11: 3.5785 L22: 3.1920 REMARK 3 L33: 1.7476 L12: 1.2926 REMARK 3 L13: 0.3658 L23: 0.1086 REMARK 3 S TENSOR REMARK 3 S11: -0.0900 S12: 0.3472 S13: -0.8093 REMARK 3 S21: 0.0391 S22: 0.1684 S23: -0.2943 REMARK 3 S31: 0.4503 S32: 0.0414 S33: 0.0301 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 173 THROUGH 313 ) REMARK 3 ORIGIN FOR THE GROUP (A): -30.5637 30.9934 13.7888 REMARK 3 T TENSOR REMARK 3 T11: 0.0791 T22: 0.1532 REMARK 3 T33: 0.1110 T12: -0.0193 REMARK 3 T13: 0.0320 T23: 0.0144 REMARK 3 L TENSOR REMARK 3 L11: 0.3346 L22: 0.2162 REMARK 3 L33: 2.6205 L12: -0.0378 REMARK 3 L13: 0.6177 L23: 0.0693 REMARK 3 S TENSOR REMARK 3 S11: 0.0409 S12: -0.0623 S13: -0.0180 REMARK 3 S21: 0.0219 S22: -0.0174 S23: 0.0442 REMARK 3 S31: -0.0084 S32: -0.4399 S33: -0.0249 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 314 THROUGH 376 ) REMARK 3 ORIGIN FOR THE GROUP (A): -13.0089 22.0577 32.1952 REMARK 3 T TENSOR REMARK 3 T11: 0.1116 T22: 0.0905 REMARK 3 T33: 0.1065 T12: -0.0133 REMARK 3 T13: 0.0173 T23: -0.0231 REMARK 3 L TENSOR REMARK 3 L11: 1.7767 L22: 1.7708 REMARK 3 L33: 2.2171 L12: 0.8453 REMARK 3 L13: 0.3003 L23: 0.1601 REMARK 3 S TENSOR REMARK 3 S11: -0.0122 S12: 0.1813 S13: -0.1218 REMARK 3 S21: 0.0111 S22: 0.0727 S23: -0.1060 REMARK 3 S31: 0.0473 S32: 0.0807 S33: -0.1005 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 5VO3 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-MAY-17. REMARK 100 THE DEPOSITION ID IS D_1000227743. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-FEB-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 19-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9794 REMARK 200 MONOCHROMATOR : DOUBLE CRYSTALS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315R REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60902 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.07300 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.98 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: MOLREP REMARK 200 STARTING MODEL: 3ISZ REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.12 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.43 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.15 M HEPES PH 7.5, 0.06 M SODIUM REMARK 280 POTASSIUM TARTRATE, 26 % PEG 8000, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: I 2 2 2 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,Y,-Z REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z+1/2 REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 X+1/2,-Y+1/2,-Z+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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 28.32400 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 67.76800 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 74.80650 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 28.32400 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 67.76800 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 74.80650 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 28.32400 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 67.76800 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 74.80650 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 28.32400 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 67.76800 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 74.80650 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: 6840 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 27930 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -151.0 KCAL/MOL 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 BIOMT1 2 -1.000000 0.000000 0.000000 -56.64800 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 691 LIES ON A SPECIAL POSITION. REMARK 375 HOH A 824 LIES ON A SPECIAL POSITION. 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 SER A -2 OG REMARK 470 ASN A -1 CG OD1 ND2 REMARK 470 MET A 1 CG SD CE REMARK 470 LYS A 123 CG CD CE NZ REMARK 470 LYS A 297 CG 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 A 757 O HOH A 821 1.91 REMARK 500 O THR A 296 O HOH A 601 2.11 REMARK 500 O HOH A 768 O HOH A 806 2.16 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 ASN A 46 -118.57 53.86 REMARK 500 MET A 101 33.01 -148.78 REMARK 500 ALA A 136 -127.79 -109.90 REMARK 500 PRO A 164 97.86 -68.83 REMARK 500 REMARK 500 REMARK: NULL 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 ZN A 503 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 HIS A 67 NE2 REMARK 620 2 ASP A 100 OD1 99.3 REMARK 620 3 GLU A 163 OE1 84.9 154.2 REMARK 620 4 GLU A 163 OE2 120.0 102.1 55.2 REMARK 620 5 SIN A 501 O2 117.7 103.2 97.0 110.7 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 504 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 100 OD2 REMARK 620 2 GLU A 135 OE1 88.9 REMARK 620 3 GLU A 135 OE2 145.0 58.0 REMARK 620 4 HIS A 349 NE2 101.7 109.1 100.0 REMARK 620 5 SIN A 501 O1 104.8 147.2 99.3 97.3 REMARK 620 6 SIN A 501 O2 92.1 95.5 81.2 151.8 55.0 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue SIN A 501 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue API A 502 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 503 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue ZN A 504 DBREF 5VO3 A 1 376 UNP P44514 DAPE_HAEIN 1 376 SEQADV 5VO3 ALA A -3 UNP P44514 EXPRESSION TAG SEQADV 5VO3 SER A -2 UNP P44514 EXPRESSION TAG SEQADV 5VO3 ASN A -1 UNP P44514 EXPRESSION TAG SEQADV 5VO3 ALA A 0 UNP P44514 EXPRESSION TAG SEQRES 1 A 380 ALA SER ASN ALA MET LYS GLU LYS VAL VAL SER LEU ALA SEQRES 2 A 380 GLN ASP LEU ILE ARG ARG PRO SER ILE SER PRO ASN ASP SEQRES 3 A 380 GLU GLY CYS GLN GLN ILE ILE ALA GLU ARG LEU GLU LYS SEQRES 4 A 380 LEU GLY PHE GLN ILE GLU TRP MET PRO PHE ASN ASP THR SEQRES 5 A 380 LEU ASN LEU TRP ALA LYS HIS GLY THR SER GLU PRO VAL SEQRES 6 A 380 ILE ALA PHE ALA GLY HIS THR ASP VAL VAL PRO THR GLY SEQRES 7 A 380 ASP GLU ASN GLN TRP SER SER PRO PRO PHE SER ALA GLU SEQRES 8 A 380 ILE ILE ASP GLY MET LEU TYR GLY ARG GLY ALA ALA ASP SEQRES 9 A 380 MET LYS GLY SER LEU ALA ALA MET ILE VAL ALA ALA GLU SEQRES 10 A 380 GLU TYR VAL LYS ALA ASN PRO ASN HIS LYS GLY THR ILE SEQRES 11 A 380 ALA LEU LEU ILE THR SER ASP GLU GLU ALA THR ALA LYS SEQRES 12 A 380 ASP GLY THR ILE HIS VAL VAL GLU THR LEU MET ALA ARG SEQRES 13 A 380 ASP GLU LYS ILE THR TYR CYS MET VAL GLY GLU PRO SER SEQRES 14 A 380 SER ALA LYS ASN LEU GLY ASP VAL VAL LYS ASN GLY ARG SEQRES 15 A 380 ARG GLY SER ILE THR GLY ASN LEU TYR ILE GLN GLY ILE SEQRES 16 A 380 GLN GLY HIS VAL ALA TYR PRO HIS LEU ALA GLU ASN PRO SEQRES 17 A 380 ILE HIS LYS ALA ALA LEU PHE LEU GLN GLU LEU THR THR SEQRES 18 A 380 TYR GLN TRP ASP LYS GLY ASN GLU PHE PHE PRO PRO THR SEQRES 19 A 380 SER LEU GLN ILE ALA ASN ILE HIS ALA GLY THR GLY SER SEQRES 20 A 380 ASN ASN VAL ILE PRO ALA GLU LEU TYR ILE GLN PHE ASN SEQRES 21 A 380 LEU ARG TYR CYS THR GLU VAL THR ASP GLU ILE ILE LYS SEQRES 22 A 380 GLN LYS VAL ALA GLU MET LEU GLU LYS HIS ASN LEU LYS SEQRES 23 A 380 TYR ARG ILE GLU TRP ASN LEU SER GLY LYS PRO PHE LEU SEQRES 24 A 380 THR LYS PRO GLY LYS LEU LEU ASP SER ILE THR SER ALA SEQRES 25 A 380 ILE GLU GLU THR ILE GLY ILE THR PRO LYS ALA GLU THR SEQRES 26 A 380 GLY GLY GLY THR SER ASP GLY ARG PHE ILE ALA LEU MET SEQRES 27 A 380 GLY ALA GLU VAL VAL GLU PHE GLY PRO LEU ASN SER THR SEQRES 28 A 380 ILE HIS LYS VAL ASN GLU CYS VAL SER VAL GLU ASP LEU SEQRES 29 A 380 GLY LYS CYS GLY GLU ILE TYR HIS LYS MET LEU VAL ASN SEQRES 30 A 380 LEU LEU ASP HET SIN A 501 12 HET API A 502 25 HET ZN A 503 1 HET ZN A 504 1 HETNAM SIN SUCCINIC ACID HETNAM API 2,6-DIAMINOPIMELIC ACID HETNAM ZN ZINC ION FORMUL 2 SIN C4 H6 O4 FORMUL 3 API C7 H14 N2 O4 FORMUL 4 ZN 2(ZN 2+) FORMUL 6 HOH *229(H2 O) HELIX 1 AA1 SER A -2 ARG A 14 1 17 HELIX 2 AA2 GLY A 24 LYS A 35 1 12 HELIX 3 AA3 ASP A 75 TRP A 79 5 5 HELIX 4 AA4 MET A 101 ASN A 119 1 19 HELIX 5 AA5 GLY A 141 ARG A 152 1 12 HELIX 6 AA6 TYR A 197 ALA A 201 5 5 HELIX 7 AA7 ASN A 203 TYR A 218 1 16 HELIX 8 AA8 THR A 264 HIS A 279 1 16 HELIX 9 AA9 GLY A 299 GLY A 314 1 16 HELIX 10 AB1 ASP A 327 LEU A 333 1 7 HELIX 11 AB2 VAL A 357 ASP A 376 1 20 SHEET 1 AA1 6 GLN A 39 TRP A 42 0 SHEET 2 AA1 6 ASN A 50 HIS A 55 -1 O LYS A 54 N GLN A 39 SHEET 3 AA1 6 THR A 125 THR A 131 -1 O ILE A 130 N LEU A 51 SHEET 4 AA1 6 VAL A 61 HIS A 67 1 N PHE A 64 O LEU A 129 SHEET 5 AA1 6 TYR A 158 VAL A 161 1 O TYR A 158 N ALA A 63 SHEET 6 AA1 6 GLU A 337 GLU A 340 1 O GLU A 337 N CYS A 159 SHEET 1 AA2 3 ILE A 88 ILE A 89 0 SHEET 2 AA2 3 MET A 92 TYR A 94 -1 O MET A 92 N ILE A 89 SHEET 3 AA2 3 CYS A 354 SER A 356 -1 O VAL A 355 N LEU A 93 SHEET 1 AA3 2 VAL A 173 LYS A 175 0 SHEET 2 AA3 2 LYS A 318 GLU A 320 1 O GLU A 320 N VAL A 174 SHEET 1 AA4 2 GLY A 177 ARG A 178 0 SHEET 2 AA4 2 PHE A 294 LEU A 295 -1 O PHE A 294 N ARG A 178 SHEET 1 AA5 4 SER A 231 HIS A 238 0 SHEET 2 AA5 4 GLU A 250 TYR A 259 -1 O TYR A 252 N HIS A 238 SHEET 3 AA5 4 GLY A 180 GLN A 189 -1 N LEU A 186 O ILE A 253 SHEET 4 AA5 4 TYR A 283 GLY A 291 -1 O ARG A 284 N TYR A 187 SHEET 1 AA6 2 GLY A 193 HIS A 194 0 SHEET 2 AA6 2 VAL A 246 ILE A 247 -1 O ILE A 247 N GLY A 193 LINK NE2 HIS A 67 ZN ZN A 503 1555 1555 2.01 LINK OD1 ASP A 100 ZN ZN A 503 1555 1555 1.97 LINK OD2 ASP A 100 ZN ZN A 504 1555 1555 1.95 LINK OE1 GLU A 135 ZN ZN A 504 1555 1555 2.03 LINK OE2 GLU A 135 ZN ZN A 504 1555 1555 2.46 LINK OE1 GLU A 163 ZN ZN A 503 1555 1555 2.59 LINK OE2 GLU A 163 ZN ZN A 503 1555 1555 2.04 LINK NE2 HIS A 349 ZN ZN A 504 1555 1555 2.09 LINK O2 SIN A 501 ZN ZN A 503 1555 1555 2.36 LINK O1 SIN A 501 ZN ZN A 504 1555 1555 2.27 LINK O2 SIN A 501 ZN ZN A 504 1555 1555 2.47 CISPEP 1 SER A 19 PRO A 20 0 -2.28 CISPEP 2 GLU A 59 PRO A 60 0 -4.94 CISPEP 3 ASP A 100 MET A 101 0 1.66 SITE 1 AC1 14 ASP A 100 GLU A 134 GLU A 135 GLU A 163 SITE 2 AC1 14 ARG A 178 HIS A 194 TYR A 197 GLY A 324 SITE 3 AC1 14 THR A 325 HIS A 349 API A 502 ZN A 503 SITE 4 AC1 14 ZN A 504 HOH A 678 SITE 1 AC2 14 GLU A 134 GLU A 135 ALA A 136 SER A 181 SITE 2 AC2 14 HIS A 194 ASN A 244 ASN A 245 ARG A 258 SITE 3 AC2 14 SER A 290 GLY A 324 THR A 325 SIN A 501 SITE 4 AC2 14 HOH A 698 HOH A 703 SITE 1 AC3 4 HIS A 67 ASP A 100 GLU A 163 SIN A 501 SITE 1 AC4 4 ASP A 100 GLU A 135 HIS A 349 SIN A 501 CRYST1 56.648 135.536 149.613 90.00 90.00 90.00 I 2 2 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 0.017653 0.000000 0.000000 0.00000 SCALE2 0.000000 0.007378 0.000000 0.00000 SCALE3 0.000000 0.000000 0.006684 0.00000