HEADER ISOMERASE 11-APR-17 5VGS TITLE CRYSTAL STRUCTURE OF LACHRYMATORY FACTOR SYNTHASE FROM ALLIUM CEPA IN TITLE 2 COMPLEX WITH CROTYL ALCOHOL COMPND MOL_ID: 1; COMPND 2 MOLECULE: LACHRYMATORY-FACTOR SYNTHASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ALLIUM CEPA; SOURCE 3 ORGANISM_COMMON: ONION; SOURCE 4 ORGANISM_TAXID: 4679; SOURCE 5 GENE: LFS; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS LACHRYMATORY FACTOR, ONION, SULFENIC ACID, CROTYL ALCOHOL, ISOMERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.A.SILVAROLI,M.J.PLESHINGER,S.BANERJEE,P.D.KISER,M.GOLCZAK REVDAT 5 04-OCT-23 5VGS 1 REMARK REVDAT 4 11-DEC-19 5VGS 1 REMARK REVDAT 3 27-SEP-17 5VGS 1 JRNL REVDAT 2 02-AUG-17 5VGS 1 JRNL REVDAT 1 26-JUL-17 5VGS 0 JRNL AUTH J.A.SILVAROLI,M.J.PLESHINGER,S.BANERJEE,P.D.KISER,M.GOLCZAK JRNL TITL ENZYME THAT MAKES YOU CRY-CRYSTAL STRUCTURE OF LACHRYMATORY JRNL TITL 2 FACTOR SYNTHASE FROM ALLIUM CEPA. JRNL REF ACS CHEM. BIOL. V. 12 2296 2017 JRNL REFN ESSN 1554-8937 JRNL PMID 28708375 JRNL DOI 10.1021/ACSCHEMBIO.7B00336 REMARK 2 REMARK 2 RESOLUTION. 1.90 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.10.1_2155: ???) 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) : 1.90 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 37.09 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.1 REMARK 3 NUMBER OF REFLECTIONS : 12510 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.167 REMARK 3 FREE R VALUE : 0.215 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.020 REMARK 3 FREE R VALUE TEST SET COUNT : 628 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 37.1000 - 3.0157 0.99 3106 160 0.1511 0.1979 REMARK 3 2 3.0157 - 2.3938 1.00 2978 161 0.1708 0.2039 REMARK 3 3 2.3938 - 2.0912 1.00 2963 143 0.1688 0.2291 REMARK 3 4 2.0912 - 1.9000 0.97 2835 164 0.2144 0.2806 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) : 21.650 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 : 0.009 1258 REMARK 3 ANGLE : 0.994 1698 REMARK 3 CHIRALITY : 0.054 181 REMARK 3 PLANARITY : 0.006 217 REMARK 3 DIHEDRAL : 16.516 739 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 5VGS COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 12-APR-17. REMARK 100 THE DEPOSITION ID IS D_1000227394. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-OCT-16 REMARK 200 TEMPERATURE (KELVIN) : 80 REMARK 200 PH : 4.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 24-ID-E REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9791 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : IMOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12549 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.900 REMARK 200 RESOLUTION RANGE LOW (A) : 40.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.4 REMARK 200 DATA REDUNDANCY : 5.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.01530 REMARK 200 FOR THE DATA SET : 6.6000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.90 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.94 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.7 REMARK 200 DATA REDUNDANCY IN SHELL : 4.40 REMARK 200 R MERGE FOR SHELL (I) : 0.90000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.500 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: 5VGL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.26 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM ACETATE, PH 4.5 REMARK 280 CONTAINING PEG 3350 AT CONCENTRATIONS BETWEEN 25%-32% (W/V), REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 19.46500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 48.81500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.05000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 48.81500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.46500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.05000 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 13 REMARK 465 SER A 14 REMARK 465 PRO A 15 REMARK 465 ALA A 169 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 394 O HOH A 451 1.89 REMARK 500 O HOH A 477 O HOH A 492 1.93 REMARK 500 O HOH A 302 O HOH A 331 2.08 REMARK 500 O HOH A 374 O HOH A 449 2.12 REMARK 500 OE1 GLU A 35 O HOH A 301 2.14 REMARK 500 O HOH A 337 O HOH A 392 2.15 REMARK 500 O ASP A 43 O HOH A 302 2.18 REMARK 500 O HOH A 436 O HOH A 439 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 LEU A 29 76.78 -119.08 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 9A4 A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue 9A7 A 202 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5VGL RELATED DB: PDB DBREF 5VGS A 25 169 UNP P59082 LFS_ALLCE 25 169 SEQADV 5VGS GLY A 13 UNP P59082 EXPRESSION TAG SEQADV 5VGS SER A 14 UNP P59082 EXPRESSION TAG SEQADV 5VGS PRO A 15 UNP P59082 EXPRESSION TAG SEQADV 5VGS GLY A 16 UNP P59082 EXPRESSION TAG SEQADV 5VGS ILE A 17 UNP P59082 EXPRESSION TAG SEQADV 5VGS SER A 18 UNP P59082 EXPRESSION TAG SEQADV 5VGS GLY A 19 UNP P59082 EXPRESSION TAG SEQADV 5VGS GLY A 20 UNP P59082 EXPRESSION TAG SEQADV 5VGS GLY A 21 UNP P59082 EXPRESSION TAG SEQADV 5VGS GLY A 22 UNP P59082 EXPRESSION TAG SEQADV 5VGS GLY A 23 UNP P59082 EXPRESSION TAG SEQADV 5VGS LYS A 24 UNP P59082 EXPRESSION TAG SEQRES 1 A 157 GLY SER PRO GLY ILE SER GLY GLY GLY GLY GLY LYS VAL SEQRES 2 A 157 HIS ALA LEU LEU PRO ASN THR LYS PRO GLU GLN ALA TRP SEQRES 3 A 157 THR LEU LEU LYS ASP PHE ILE ASN LEU HIS LYS VAL MET SEQRES 4 A 157 PRO SER LEU SER VAL CYS GLU LEU VAL GLU GLY GLU ALA SEQRES 5 A 157 ASN VAL VAL GLY CYS VAL ARG TYR VAL LYS GLY ILE MET SEQRES 6 A 157 HIS PRO ILE GLU GLU GLU PHE TRP ALA LYS GLU LYS LEU SEQRES 7 A 157 VAL ALA LEU ASP ASN LYS ASN MET SER TYR SER TYR ILE SEQRES 8 A 157 PHE THR GLU CYS PHE THR GLY TYR GLU ASP TYR THR ALA SEQRES 9 A 157 THR MET GLN ILE VAL GLU GLY PRO GLU HIS LYS GLY SER SEQRES 10 A 157 ARG PHE ASP TRP SER PHE GLN CYS LYS TYR ILE GLU GLY SEQRES 11 A 157 MET THR GLU SER ALA PHE THR GLU ILE LEU GLN HIS TRP SEQRES 12 A 157 ALA THR GLU ILE GLY GLN LYS ILE GLU GLU VAL CYS SER SEQRES 13 A 157 ALA HET 9A4 A 201 12 HET 9A7 A 202 14 HETNAM 9A4 (2Z)-BUT-2-EN-1-OL HETNAM 9A7 (2E)-BUT-2-EN-1-OL FORMUL 2 9A4 C4 H8 O FORMUL 3 9A7 C4 H8 O FORMUL 4 HOH *202(H2 O) HELIX 1 AA1 LYS A 33 LYS A 42 1 10 HELIX 2 AA2 ASP A 43 MET A 51 5 9 HELIX 3 AA3 PRO A 124 LYS A 127 5 4 HELIX 4 AA4 THR A 144 CYS A 167 1 24 SHEET 1 AA1 7 GLY A 21 LEU A 29 0 SHEET 2 AA1 7 SER A 129 CYS A 137 -1 O TRP A 133 N VAL A 25 SHEET 3 AA1 7 THR A 115 GLU A 122 -1 N GLN A 119 O ASP A 132 SHEET 4 AA1 7 SER A 99 CYS A 107 -1 N TYR A 102 O ALA A 116 SHEET 5 AA1 7 GLU A 82 ASP A 94 -1 N ASP A 94 O SER A 99 SHEET 6 AA1 7 VAL A 70 MET A 77 -1 N MET A 77 O GLU A 82 SHEET 7 AA1 7 LEU A 54 GLU A 61 -1 N GLU A 58 O TYR A 72 SHEET 1 AA2 2 TYR A 111 GLU A 112 0 SHEET 2 AA2 2 TYR A 139 ILE A 140 -1 O TYR A 139 N GLU A 112 CISPEP 1 HIS A 78 PRO A 79 0 -0.59 SITE 1 AC1 6 PHE A 84 GLU A 88 TYR A 102 TYR A 114 SITE 2 AC1 6 PHE A 148 9A7 A 202 SITE 1 AC2 7 PHE A 84 GLU A 88 TYR A 102 TYR A 114 SITE 2 AC2 7 ALA A 116 TRP A 133 9A4 A 201 CRYST1 38.930 40.100 97.630 90.00 90.00 90.00 P 21 21 21 4 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 0.025687 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024938 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010243 0.00000