HEADER METAL BINDING PROTEIN 04-AUG-17 5ONO TITLE CRYSTAL STRUCTURE OF ECTOINE SYNTHASE FROM P. LAUTUS COMPND MOL_ID: 1; COMPND 2 MOLECULE: L-ECTOINE SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: N-ACETYLDIAMINOBUTYRATE DEHYDRATASE; COMPND 5 EC: 4.2.1.108; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: PAENIBACILLUS LAUTUS; SOURCE 3 ORGANISM_TAXID: 1401; SOURCE 4 GENE: ECTC, BK123_26285; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS ECTOINE, SYNTHASE, OSMOLYTE, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR E.BREMER REVDAT 4 17-JAN-24 5ONO 1 REMARK REVDAT 3 16-OCT-19 5ONO 1 REMARK REVDAT 2 06-MAR-19 5ONO 1 JRNL REVDAT 1 22-AUG-18 5ONO 0 JRNL AUTH L.CZECH,A.HOPPNER,S.KOBUS,A.SEUBERT,R.RICLEA,J.S.DICKSCHAT, JRNL AUTH 2 J.HEIDER,S.H.J.SMITS,E.BREMER JRNL TITL ILLUMINATING THE CATALYTIC CORE OF ECTOINE SYNTHASE THROUGH JRNL TITL 2 STRUCTURAL AND BIOCHEMICAL ANALYSIS. JRNL REF SCI REP V. 9 364 2019 JRNL REFN ESSN 2045-2322 JRNL PMID 30674920 JRNL DOI 10.1038/S41598-018-36247-W REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 46.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 3.220 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 7280 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 9.990 REMARK 3 FREE R VALUE TEST SET COUNT : 727 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 46.0150 - 4.2742 1.00 1386 149 0.1786 0.2142 REMARK 3 2 4.2742 - 3.3929 1.00 1310 148 0.1737 0.2274 REMARK 3 3 3.3929 - 2.9641 0.99 1297 146 0.1961 0.2476 REMARK 3 4 2.9641 - 2.6931 0.99 1286 141 0.2034 0.2669 REMARK 3 5 2.6931 - 2.5001 0.99 1274 143 0.1851 0.2824 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) : 0.250 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.660 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 : 0.014 1138 REMARK 3 ANGLE : 1.481 1547 REMARK 3 CHIRALITY : 0.054 171 REMARK 3 PLANARITY : 0.005 199 REMARK 3 DIHEDRAL : 15.288 415 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 5ONO COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 04-AUG-17. REMARK 100 THE DEPOSITION ID IS D_1200006091. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-OCT-15 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.0-5.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.988 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 2M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7282 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 46.010 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 200 DATA REDUNDANCY : 5.400 REMARK 200 R MERGE (I) : 0.08200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 8.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: 5BXX REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 61.86 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.22 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2 M AMMONIUM SULFATE, 0.1 M REMARK 280 PHOSPHATE CITRATE PH 4.2, 20% (V/V) PEG 300, 10% (V/V) GLYCEROL., REMARK 280 BATCH MODE, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-Z+1/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 22.94600 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 45.89200 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 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 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 45.89200 REMARK 290 SMTRY1 6 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 22.94600 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8090 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 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 4CS A 202 O HOH A 301 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 339 O HOH A 342 6767 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 ASP A 130 40.87 -93.39 REMARK 500 PHE A 137 -0.92 -151.83 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PHE A 137 GLU A 138 139.39 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue FE A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 4CS A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5ONN RELATED DB: PDB DBREF1 5ONO A 1 130 UNP A0A1R1AV52_PAELA DBREF2 5ONO A A0A1R1AV52 1 130 SEQADV 5ONO THR A 19 UNP A0A1R1AV5 LYS 19 CONFLICT SEQADV 5ONO VAL A 71 UNP A0A1R1AV5 ILE 71 CONFLICT SEQADV 5ONO THR A 79 UNP A0A1R1AV5 SER 79 CONFLICT SEQADV 5ONO THR A 129 UNP A0A1R1AV5 SER 129 CONFLICT SEQADV 5ONO ASN A 131 UNP A0A1R1AV5 EXPRESSION TAG SEQADV 5ONO TRP A 132 UNP A0A1R1AV5 EXPRESSION TAG SEQADV 5ONO SER A 133 UNP A0A1R1AV5 EXPRESSION TAG SEQADV 5ONO HIS A 134 UNP A0A1R1AV5 EXPRESSION TAG SEQADV 5ONO PRO A 135 UNP A0A1R1AV5 EXPRESSION TAG SEQADV 5ONO GLN A 136 UNP A0A1R1AV5 EXPRESSION TAG SEQADV 5ONO PHE A 137 UNP A0A1R1AV5 EXPRESSION TAG SEQADV 5ONO GLU A 138 UNP A0A1R1AV5 EXPRESSION TAG SEQRES 1 A 138 MET ILE VAL LYS HIS LEU GLU GLU ILE VAL ASP THR LYS SEQRES 2 A 138 ASP ASP ILE ASP THR THR THR TRP ASN SER ARG ARG LEU SEQRES 3 A 138 LEU LEU THR LYS ASP GLY MET GLY PHE SER LEU ASN ASP SEQRES 4 A 138 THR LEU ILE LYS ALA GLY THR GLU THR LEU ILE TRP TYR SEQRES 5 A 138 LYS ASN HIS VAL GLU ALA VAL TYR CYS ILE GLU GLY GLU SEQRES 6 A 138 GLY GLU ILE GLU VAL VAL GLY GLY GLU THR TYR PRO ILE SEQRES 7 A 138 THR PRO GLY MET MET TYR ALA LEU ASP GLY HIS GLU LYS SEQRES 8 A 138 HIS TYR LEU ARG ALA ARG SER GLN MET ARG MET VAL CYS SEQRES 9 A 138 VAL PHE ASN PRO PRO LEU THR GLY ALA GLU VAL HIS ASP SEQRES 10 A 138 GLU GLU GLY THR TYR PRO LEU LEU ALA PRO ILE THR ASP SEQRES 11 A 138 ASN TRP SER HIS PRO GLN PHE GLU HET FE A 201 1 HET 4CS A 202 19 HETNAM FE FE (III) ION HETNAM 4CS (4S)-2-METHYL-1,4,5,6-TETRAHYDROPYRIMIDINE-4-CARBOXYLIC HETNAM 2 4CS ACID HETSYN 4CS ECTOINE FORMUL 2 FE FE 3+ FORMUL 3 4CS C6 H10 N2 O2 FORMUL 4 HOH *42(H2 O) HELIX 1 AA1 HIS A 5 VAL A 10 1 6 HELIX 2 AA2 LEU A 28 GLY A 32 5 5 HELIX 3 AA3 THR A 111 GLU A 118 1 8 SHEET 1 AA1 6 ASP A 15 ASP A 17 0 SHEET 2 AA1 6 TRP A 21 LEU A 27 -1 O SER A 23 N ILE A 16 SHEET 3 AA1 6 SER A 36 ILE A 42 -1 O LEU A 37 N LEU A 26 SHEET 4 AA1 6 MET A 100 ASN A 107 -1 O MET A 102 N THR A 40 SHEET 5 AA1 6 VAL A 56 GLU A 63 -1 N TYR A 60 O VAL A 103 SHEET 6 AA1 6 MET A 83 ALA A 85 -1 O TYR A 84 N VAL A 59 SHEET 1 AA2 5 THR A 75 ILE A 78 0 SHEET 2 AA2 5 GLY A 66 VAL A 70 -1 N GLY A 66 O ILE A 78 SHEET 3 AA2 5 HIS A 92 ALA A 96 -1 O ARG A 95 N GLU A 67 SHEET 4 AA2 5 GLU A 47 ILE A 50 -1 N ILE A 50 O HIS A 92 SHEET 5 AA2 5 THR A 121 LEU A 125 -1 O LEU A 124 N GLU A 47 CISPEP 1 ASN A 107 PRO A 108 0 -1.47 SITE 1 AC1 4 GLU A 57 TYR A 84 HIS A 92 4CS A 202 SITE 1 AC2 11 TRP A 21 SER A 23 ASN A 38 THR A 40 SITE 2 AC2 11 TYR A 52 GLU A 57 CYS A 104 PHE A 106 SITE 3 AC2 11 FE A 201 HOH A 301 HOH A 309 CRYST1 71.418 71.418 68.838 90.00 90.00 120.00 P 31 2 1 6 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 0.014002 0.008084 0.000000 0.00000 SCALE2 0.000000 0.016168 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014527 0.00000