HEADER LIGASE 07-DEC-16 5MLP TITLE STRUCTURE OF CDPS FROM RICKETTSIELLA GRYLLI COMPND MOL_ID: 1; COMPND 2 MOLECULE: UNCHARACTERIZED PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: RICKETTSIELLA GRYLLI; SOURCE 3 ORGANISM_TAXID: 59196; SOURCE 4 GENE: RICGR_1344; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS CYCLODIPEPTIDE SYNTHASE, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR G.BOURGEOIS,J.SEGUIN,M.MOUTIEZ,M.BABIN,P.BELIN,Y.MECHULAM,M.GONDRY, AUTHOR 2 E.SCHMITT REVDAT 2 15-MAY-19 5MLP 1 JRNL REVDAT 1 02-MAY-18 5MLP 0 JRNL AUTH G.BOURGEOIS,J.SEGUIN,M.BABIN,P.BELIN,M.MOUTIEZ,Y.MECHULAM, JRNL AUTH 2 M.GONDRY,E.SCHMITT JRNL TITL STRUCTURAL BASIS FOR PARTITION OF THE CYCLODIPEPTIDE JRNL TITL 2 SYNTHASES INTO TWO SUBFAMILIES. JRNL REF J.STRUCT.BIOL. V. 203 17 2018 JRNL REFN ESSN 1095-8657 JRNL PMID 29505829 JRNL DOI 10.1016/J.JSB.2018.03.001 REMARK 2 REMARK 2 RESOLUTION. 1.99 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) : 1.99 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.43 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 16958 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.250 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.990 REMARK 3 FREE R VALUE TEST SET COUNT : 846 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 40.4351 - 3.6153 1.00 2759 160 0.1580 0.1742 REMARK 3 2 3.6153 - 2.8698 1.00 2711 148 0.2008 0.2948 REMARK 3 3 2.8698 - 2.5071 1.00 2713 147 0.2360 0.3244 REMARK 3 4 2.5071 - 2.2779 1.00 2718 128 0.2437 0.2968 REMARK 3 5 2.2779 - 2.1146 1.00 2722 123 0.2664 0.3688 REMARK 3 6 2.1146 - 1.9900 0.93 2489 140 0.3209 0.3748 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) : 0.300 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 34.110 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 31.30 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 2133 REMARK 3 ANGLE : 0.993 2865 REMARK 3 CHIRALITY : 0.042 307 REMARK 3 PLANARITY : 0.004 367 REMARK 3 DIHEDRAL : 15.258 805 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 5MLP COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 07-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1200002653. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 12-APR-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SOLEIL REMARK 200 BEAMLINE : PROXIMA 1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9786 REMARK 200 MONOCHROMATOR : CRYSTAL 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 : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 17008 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.990 REMARK 200 RESOLUTION RANGE LOW (A) : 45.650 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.5 REMARK 200 DATA REDUNDANCY : 4.490 REMARK 200 R MERGE (I) : 0.12000 REMARK 200 R SYM (I) : 0.12000 REMARK 200 FOR THE DATA SET : 7.0200 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.99 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 93.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.38 REMARK 200 R MERGE FOR SHELL (I) : 0.96000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.180 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: NA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 38.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.01 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG3350 15% POTASSIUM FLUORIDE 0.2M, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 278K 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 31.52950 REMARK 290 SMTRY3 2 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: 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: 13880 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 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 0 REMARK 465 ALA A 1 REMARK 465 ARG A 2 REMARK 465 ASN A 120 REMARK 465 GLN A 121 REMARK 465 ILE A 122 REMARK 465 GLU A 123 REMARK 465 HIS A 262 REMARK 465 HIS A 263 REMARK 465 HIS A 264 REMARK 465 HIS A 265 REMARK 465 HIS A 266 REMARK 465 HIS A 267 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 OD2 ASP A 141 OH TYR A 212 2.11 REMARK 500 O HOH A 377 O HOH A 379 2.13 REMARK 500 O HOH A 367 O HOH A 382 2.18 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 LYS A 244 48.31 -86.35 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4Q24 RELATED DB: PDB DBREF 5MLP A 2 259 UNP A8PPN3 A8PPN3_9COXI 2 259 SEQADV 5MLP MET A 0 UNP A8PPN3 INITIATING METHIONINE SEQADV 5MLP ALA A 1 UNP A8PPN3 EXPRESSION TAG SEQADV 5MLP ARG A 260 UNP A8PPN3 EXPRESSION TAG SEQADV 5MLP SER A 261 UNP A8PPN3 EXPRESSION TAG SEQADV 5MLP HIS A 262 UNP A8PPN3 EXPRESSION TAG SEQADV 5MLP HIS A 263 UNP A8PPN3 EXPRESSION TAG SEQADV 5MLP HIS A 264 UNP A8PPN3 EXPRESSION TAG SEQADV 5MLP HIS A 265 UNP A8PPN3 EXPRESSION TAG SEQADV 5MLP HIS A 266 UNP A8PPN3 EXPRESSION TAG SEQADV 5MLP HIS A 267 UNP A8PPN3 EXPRESSION TAG SEQRES 1 A 268 MET ALA ARG TYR LYS LYS MET LYS LYS ALA LYS PHE GLN SEQRES 2 A 268 GLY ASN VAL ASP ILE ILE LYS ASN ALA GLN CYS LEU LEU SEQRES 3 A 268 MET GLY ILE SER MET ASN GLN THR HIS GLN SER GLY GLU SEQRES 4 A 268 GLU LEU TYR ALA PHE ILE ASN GLU ILE LYS LYS TYR THR SEQRES 5 A 268 ASN ILE LYS LYS VAL ILE PHE VAL ILE THR ASP TYR LEU SEQRES 6 A 268 HIS ARG HIS TYR VAL GLN LEU GLU THR GLY LEU PRO LEU SEQRES 7 A 268 GLU GLU ALA GLY LYS GLU ALA GLU LYS MET GLY GLU SER SEQRES 8 A 268 TRP LEU GLN LEU ASN GLU ALA SER LEU ASN SER LEU SER SEQRES 9 A 268 PRO VAL GLU LEU GLN LEU VAL GLN TRP LYS SER LEU VAL SEQRES 10 A 268 GLU GLY SER ASN GLN ILE GLU ASP THR SER TYR SER ASP SEQRES 11 A 268 CYS LEU SER LYS THR GLU ASN CYS TYR ARG ASP ASP PRO SEQRES 12 A 268 PHE PHE GLN GLN MET VAL ASP THR TYR SER ASN GLU PHE SEQRES 13 A 268 GLY GLN LYS HIS CYS ASN ARG LEU LYS ASN ARG ILE GLU SEQRES 14 A 268 ILE THR LEU GLU ALA CYS GLN GLN ALA ALA LYS ASN TYR SEQRES 15 A 268 PHE LEU GLU GLU SER THR ILE ILE LEU LYS PHE ILE SER SEQRES 16 A 268 LEU ASN PHE ASP VAL ILE THR TYR PRO GLY LYS CYS ASN SEQRES 17 A 268 GLN GLY ILE ASN TYR ILE TYR ASN LYS TYR ILE GLY LYS SEQRES 18 A 268 PRO LEU ASN PHE ILE SER TYR ARG PHE ARG SER GLU HIS SEQRES 19 A 268 VAL LYS ASN SER LEU PHE SER PHE SER LYS LYS THR GLU SEQRES 20 A 268 GLU SER ILE ASN ASP ALA HIS GLN PHE ARG ARG ASN ILE SEQRES 21 A 268 ARG SER HIS HIS HIS HIS HIS HIS FORMUL 2 HOH *85(H2 O) HELIX 1 AA1 VAL A 15 ASN A 20 1 6 HELIX 2 AA2 GLY A 37 LYS A 48 1 12 HELIX 3 AA3 ASP A 62 LEU A 64 5 3 HELIX 4 AA4 HIS A 65 GLY A 74 1 10 HELIX 5 AA5 PRO A 76 ASN A 95 1 20 HELIX 6 AA6 ASN A 95 LEU A 102 1 8 HELIX 7 AA7 TRP A 112 GLY A 118 1 7 HELIX 8 AA8 THR A 125 ASP A 141 1 17 HELIX 9 AA9 ASP A 141 LYS A 164 1 24 HELIX 10 AB1 THR A 170 ILE A 193 1 24 HELIX 11 AB2 SER A 194 ASN A 196 5 3 HELIX 12 AB3 ASN A 207 GLY A 219 1 13 HELIX 13 AB4 SER A 248 ILE A 259 1 12 SHEET 1 AA1 6 MET A 6 PHE A 11 0 SHEET 2 AA1 6 PHE A 224 GLU A 232 -1 O ARG A 230 N LYS A 8 SHEET 3 AA1 6 VAL A 199 TYR A 202 1 N ILE A 200 O ILE A 225 SHEET 4 AA1 6 CYS A 23 SER A 29 1 N LEU A 25 O VAL A 199 SHEET 5 AA1 6 LYS A 55 THR A 61 1 O ILE A 57 N LEU A 24 SHEET 6 AA1 6 GLU A 106 GLN A 111 1 O VAL A 110 N ILE A 60 SSBOND 1 CYS A 160 CYS A 174 1555 1555 2.06 CISPEP 1 SER A 103 PRO A 104 0 11.70 CRYST1 43.936 63.059 49.615 90.00 113.06 90.00 P 1 21 1 2 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 0.022760 0.000000 0.009687 0.00000 SCALE2 0.000000 0.015858 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021905 0.00000