HEADER RNA BINDING PROTEIN 17-NOV-20 7AZU TITLE CRYSTAL STRUCTURE OF A CYCLODIPEPTIDE SYNTHASE FROM BACILLUS TITLE 2 THERMOAMYLOVORANS COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYCLODIPEPTIDE SYNTHASE, BTCDPS; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS THERMOAMYLOVORANS; SOURCE 3 ORGANISM_TAXID: 35841; SOURCE 4 GENE: YVMC, BT1A1_1686; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS CDPS, CYCLODIPEPTIDE SYNTHASE, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.J.HARDING,C.M.CZEKSTER REVDAT 3 31-JAN-24 7AZU 1 REMARK REVDAT 2 19-MAY-21 7AZU 1 JRNL REVDAT 1 27-JAN-21 7AZU 0 JRNL AUTH C.J.HARDING,E.SUTHERLAND,J.G.HANNA,D.R.HOUSTON,C.M.CZEKSTER JRNL TITL BYPASSING THE REQUIREMENT FOR AMINOACYL-TRNA BY A JRNL TITL 2 CYCLODIPEPTIDE SYNTHASE ENZYME. JRNL REF RSC CHEM BIOL V. 2 230 2021 JRNL REFN ESSN 2633-0679 JRNL PMID 33937777 JRNL DOI 10.1039/D0CB00142B REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14_3260 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) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 28273 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) : 0.204 REMARK 3 FREE R VALUE : 0.226 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1431 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 2.4438 - 2.2687 1.00 2663 154 0.2235 0.2538 REMARK 3 2 2.2687 - 2.1349 1.00 2659 138 0.2261 0.2844 REMARK 3 3 2.1349 - 2.0280 1.00 2643 129 0.2365 0.2498 REMARK 3 4 2.0280 - 1.9397 0.99 2639 137 0.2458 0.3040 REMARK 3 5 1.9397 - 1.8650 0.99 2614 154 0.2731 0.2839 REMARK 3 6 1.8650 - 1.8010 0.99 2606 142 0.3090 0.3701 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 26.160 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 36.46 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.48 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 : NULL NULL REMARK 3 ANGLE : NULL NULL REMARK 3 CHIRALITY : NULL NULL REMARK 3 PLANARITY : NULL NULL REMARK 3 DIHEDRAL : NULL NULL 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 7AZU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 17-NOV-20. REMARK 100 THE DEPOSITION ID IS D_1292112359. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 15-OCT-20 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 : DIAMOND REMARK 200 BEAMLINE : I03 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9762 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XIA2 REMARK 200 DATA SCALING SOFTWARE : XIA2 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 28430 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 60.500 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 26.40 REMARK 200 R MERGE (I) : 0.05900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 26.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.83 REMARK 200 COMPLETENESS FOR SHELL (%) : 97.8 REMARK 200 DATA REDUNDANCY IN SHELL : 23.90 REMARK 200 R MERGE FOR SHELL (I) : 2.13900 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.400 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: 6ZTU REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 54.59 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.71 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M NA CITRATE PH 5.5, 37% PEG 550 REMARK 280 MME, 5% 1,2-HEXANEDIOL, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 41 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+1/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+3/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+1/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+3/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-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 46.41000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.89000 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.89000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 23.20500 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.89000 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.89000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 69.61500 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.89000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.89000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 23.20500 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.89000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.89000 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 69.61500 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 46.41000 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: 11530 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 GLY A 0 REMARK 465 MET A 1 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 482 O HOH A 508 2.07 REMARK 500 OH TYR A 22 O HOH A 401 2.08 REMARK 500 O HOH A 440 O HOH A 499 2.11 REMARK 500 O HOH A 485 O HOH A 497 2.15 REMARK 500 O HOH A 484 O HOH A 489 2.18 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 479 O HOH A 492 3555 1.98 REMARK 500 O HOH A 470 O HOH A 493 8555 1.99 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 SER A 185 33.15 -148.22 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 0RE A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6ZTU RELATED DB: PDB REMARK 900 WT ENZYME REMARK 900 RELATED ID: 6ZU3 RELATED DB: PDB REMARK 900 S33C MUTANT DBREF1 7AZU A 1 231 UNP A0A090KS30_9BACI DBREF2 7AZU A A0A090KS30 1 231 SEQADV 7AZU GLY A 0 UNP A0A090KS3 EXPRESSION TAG SEQADV 7AZU ALA A 153 UNP A0A090KS3 ARG 153 ENGINEERED MUTATION SEQRES 1 A 232 GLY MET GLN GLN VAL ILE LYS ASP LEU PHE TYR VAL VAL SEQRES 2 A 232 PRO LEU SER ARG ASN CYS GLU LYS ILE TYR LYS ASN LYS SEQRES 3 A 232 THR HIS ILE LEU LEU GLY ILE SER PRO PHE ASN SER LYS SEQRES 4 A 232 PHE SER GLN ASN TYR ILE HIS GLN LEU ILE ASP TRP SER SEQRES 5 A 232 SER LYS ASN PHE LYS ASN VAL THR VAL LEU LEU ALA GLY SEQRES 6 A 232 ASP GLU ALA LYS ASN LEU LEU GLU ALA LEU GLY THR PRO SEQRES 7 A 232 THR THR LYS ALA GLU ARG LYS VAL ARG LYS GLU ILE ARG SEQRES 8 A 232 ARG HIS PHE ARG PHE SER GLU GLU ALA LEU ARG LYS ASN SEQRES 9 A 232 GLY ARG GLU ILE ASP ILE TYR THR PHE SER ASP PHE LYS SEQRES 10 A 232 ASN ASN LYS ILE TYR ASN GLU VAL TYR GLN ASN VAL ILE SEQRES 11 A 232 TYR TYR PHE GLU LYS ASP GLU LYS PHE ARG LYS SER CYS SEQRES 12 A 232 LEU ALA MET SER HIS ASP ALA LEU SER SER ALA ALA LYS SEQRES 13 A 232 SER LEU ASN MET GLU ASP ILE GLU ILE THR ASP ASN MET SEQRES 14 A 232 LEU PHE HIS ALA VAL LYS TYR VAL LEU ALA GLU LEU PRO SEQRES 15 A 232 PHE PHE LEU SER GLY ALA SER ILE LEU GLY TYR LYS GLU SEQRES 16 A 232 SER VAL LEU ALA TYR HIS ARG PRO TRP LYS LEU GLY GLU SEQRES 17 A 232 LYS ILE LYS ASN SER GLU PHE TYR ILE LYS MET SER ASP SEQRES 18 A 232 ASN GLN GLY TYR ILE ILE LEU LYS GLN ILE ASN HET 0RE A 301 8 HETNAM 0RE (2S)-HEXANE-1,2-DIOL FORMUL 2 0RE C6 H14 O2 FORMUL 3 HOH *108(H2 O) HELIX 1 AA1 GLN A 2 ASP A 7 1 6 HELIX 2 AA2 SER A 15 LYS A 25 1 11 HELIX 3 AA3 SER A 40 PHE A 55 1 16 HELIX 4 AA4 GLU A 66 LEU A 74 1 9 HELIX 5 AA5 PRO A 77 ASN A 103 1 27 HELIX 6 AA6 ASN A 118 ASP A 135 1 18 HELIX 7 AA7 ASP A 135 LEU A 157 1 23 HELIX 8 AA8 THR A 165 GLY A 191 1 27 HELIX 9 AA9 TRP A 203 ASN A 211 1 9 SHEET 1 AA1 6 TYR A 10 PRO A 13 0 SHEET 2 AA1 6 GLN A 222 LYS A 228 -1 O LYS A 228 N TYR A 10 SHEET 3 AA1 6 SER A 195 TYR A 199 1 N TYR A 199 O LEU A 227 SHEET 4 AA1 6 HIS A 27 GLY A 31 1 N LEU A 29 O ALA A 198 SHEET 5 AA1 6 ASN A 57 LEU A 62 1 O LEU A 61 N LEU A 30 SHEET 6 AA1 6 ILE A 109 THR A 111 1 O TYR A 110 N LEU A 62 SITE 1 AC1 8 ILE A 32 SER A 33 LEU A 62 ALA A 63 SITE 2 AC1 8 GLU A 179 PHE A 183 TYR A 199 HOH A 416 CRYST1 79.780 79.780 92.820 90.00 90.00 90.00 P 41 21 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 0.012534 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012534 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010774 0.00000