HEADER LYASE 03-APR-15 4Z5S TITLE CRYSTAL STRUCTURE OF APO-FORM OF ALDEHYDE DEFORMYLATING OXYGENASE FROM TITLE 2 SYNECHOCYSTIS SP.PCC 6803 COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALDEHYDE DECARBONYLASE; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AD,FATTY ALDEHYDE DECARBONYLASE; COMPND 5 EC: 4.1.99.5; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCYSTIS SP. (STRAIN PCC 6803 / KAZUSA); SOURCE 3 ORGANISM_TAXID: 1111708; SOURCE 4 STRAIN: PCC 6803 / KAZUSA; SOURCE 5 GENE: SLL0208; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS OXYGENASE, LYASE EXPDTA X-RAY DIFFRACTION AUTHOR C.JIA,M.LI,W.CHANG REVDAT 3 08-NOV-23 4Z5S 1 REMARK REVDAT 2 05-APR-17 4Z5S 1 JRNL REVDAT 1 06-APR-16 4Z5S 0 JRNL AUTH Q.WANG,L.BAO,C.JIA,M.LI,J.J.LI,X.LU JRNL TITL IDENTIFICATION OF RESIDUES IMPORTANT FOR THE ACTIVITY OF JRNL TITL 2 ALDEHYDE-DEFORMYLATING OXYGENASE THROUGH INVESTIGATION INTO JRNL TITL 3 THE STRUCTURE-ACTIVITY RELATIONSHIP JRNL REF BMC BIOTECHNOL. V. 17 31 2017 JRNL REFN ESSN 1472-6750 JRNL PMID 28302170 JRNL DOI 10.1186/S12896-017-0351-8 REMARK 2 REMARK 2 RESOLUTION. 1.58 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.8.1_1168 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) : 1.58 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 44.01 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 97.1 REMARK 3 NUMBER OF REFLECTIONS : 29825 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.175 REMARK 3 R VALUE (WORKING SET) : 0.173 REMARK 3 FREE R VALUE : 0.213 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1491 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 44.0305 - 3.5174 0.98 2795 140 0.1764 0.2082 REMARK 3 2 3.5174 - 2.7920 1.00 2670 147 0.1766 0.2271 REMARK 3 3 2.7920 - 2.4391 1.00 2664 149 0.1775 0.2044 REMARK 3 4 2.4391 - 2.2161 1.00 2646 142 0.1657 0.2196 REMARK 3 5 2.2161 - 2.0573 1.00 2649 143 0.1566 0.1976 REMARK 3 6 2.0573 - 1.9360 1.00 2625 134 0.1608 0.1844 REMARK 3 7 1.9360 - 1.8390 1.00 2626 125 0.1755 0.2119 REMARK 3 8 1.8390 - 1.7590 1.00 2611 137 0.1814 0.2130 REMARK 3 9 1.7590 - 1.6913 0.99 2587 146 0.1829 0.2332 REMARK 3 10 1.6913 - 1.6329 0.94 2438 126 0.1801 0.2496 REMARK 3 11 1.6329 - 1.5818 0.78 2023 102 0.1782 0.2243 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) : 0.130 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 19.550 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 : 0.007 1873 REMARK 3 ANGLE : 1.002 2535 REMARK 3 CHIRALITY : 0.070 270 REMARK 3 PLANARITY : 0.005 333 REMARK 3 DIHEDRAL : 13.616 712 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 14.2667 102.1311 46.6198 REMARK 3 T TENSOR REMARK 3 T11: 0.0686 T22: 0.0722 REMARK 3 T33: 0.0587 T12: -0.0160 REMARK 3 T13: -0.0021 T23: 0.0120 REMARK 3 L TENSOR REMARK 3 L11: 1.2215 L22: 1.1979 REMARK 3 L33: 0.5045 L12: -0.7584 REMARK 3 L13: -0.3012 L23: 0.2945 REMARK 3 S TENSOR REMARK 3 S11: -0.0315 S12: -0.0270 S13: -0.1187 REMARK 3 S21: -0.0712 S22: -0.0080 S23: 0.0950 REMARK 3 S31: 0.0184 S32: -0.0073 S33: 0.0235 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: SF FILE CONTAINS FRIEDEL PAIRS UNDER REMARK 3 I/F_MINUS AND I/F_PLUS COLUMNS. REMARK 4 REMARK 4 4Z5S COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-APR-15. REMARK 100 THE DEPOSITION ID IS D_1000208522. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 08-JAN-12 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.2 REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL17U REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.98 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29825 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.582 REMARK 200 RESOLUTION RANGE LOW (A) : 44.014 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 200 DATA REDUNDANCY : 8.500 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 22.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.58 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.61 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.7 REMARK 200 DATA REDUNDANCY IN SHELL : 9.10 REMARK 200 R MERGE FOR SHELL (I) : 0.49700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 4.750 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: 2OC5 REMARK 200 REMARK 200 REMARK: THE ENTRY CONTAINS FRIEDEL PAIRS IN F_PLUS/MINUS COLUMNS. REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.04 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 19%(V/V) 2-PROPANOL, 0.2M AMMONIUM REMARK 280 SULFATE, 0.1M SODIUM CITRATE TRIBASIC DEHYDRATE PH5.2, 18% REMARK 280 PEG3350, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 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+1/2,Y+1/2,-Z 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 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 34.25950 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 44.01350 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 34.25950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 44.01350 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 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 1 REMARK 465 PRO A 2 REMARK 465 GLU A 3 REMARK 465 LEU A 4 REMARK 465 ALA A 5 REMARK 465 ALA A 229 REMARK 465 GLY A 230 REMARK 465 VAL A 231 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 518 O HOH A 531 2.10 REMARK 500 O HOH A 509 O HOH A 518 2.12 REMARK 500 O HOH A 476 O HOH A 531 2.13 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 340 O HOH A 367 2675 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 112 -65.32 -107.08 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 581 DISTANCE = 5.97 ANGSTROMS REMARK 525 HOH A 582 DISTANCE = 6.47 ANGSTROMS DBREF 4Z5S A 1 231 UNP Q55688 ALDEC_SYNY3 1 231 SEQRES 1 A 231 MET PRO GLU LEU ALA VAL ARG THR GLU PHE ASP TYR SER SEQRES 2 A 231 SER GLU ILE TYR LYS ASP ALA TYR SER ARG ILE ASN ALA SEQRES 3 A 231 ILE VAL ILE GLU GLY GLU GLN GLU ALA TYR SER ASN TYR SEQRES 4 A 231 LEU GLN MET ALA GLU LEU LEU PRO GLU ASP LYS GLU GLU SEQRES 5 A 231 LEU THR ARG LEU ALA LYS MET GLU ASN ARG HIS LYS LYS SEQRES 6 A 231 GLY PHE GLN ALA CYS GLY ASN ASN LEU GLN VAL ASN PRO SEQRES 7 A 231 ASP MET PRO TYR ALA GLN GLU PHE PHE ALA GLY LEU HIS SEQRES 8 A 231 GLY ASN PHE GLN HIS ALA PHE SER GLU GLY LYS VAL VAL SEQRES 9 A 231 THR CYS LEU LEU ILE GLN ALA LEU ILE ILE GLU ALA PHE SEQRES 10 A 231 ALA ILE ALA ALA TYR ASN ILE TYR ILE PRO VAL ALA ASP SEQRES 11 A 231 ASP PHE ALA ARG LYS ILE THR GLU GLY VAL VAL LYS ASP SEQRES 12 A 231 GLU TYR THR HIS LEU ASN TYR GLY GLU GLU TRP LEU LYS SEQRES 13 A 231 ALA ASN PHE ALA THR ALA LYS GLU GLU LEU GLU GLN ALA SEQRES 14 A 231 ASN LYS GLU ASN LEU PRO LEU VAL TRP LYS MET LEU ASN SEQRES 15 A 231 GLN VAL GLN GLY ASP ALA LYS VAL LEU GLY MET GLU LYS SEQRES 16 A 231 GLU ALA LEU VAL GLU ASP PHE MET ILE SER TYR GLY GLU SEQRES 17 A 231 ALA LEU SER ASN ILE GLY PHE SER THR ARG GLU ILE MET SEQRES 18 A 231 ARG MET SER SER TYR GLY LEU ALA GLY VAL FORMUL 2 HOH *282(H2 O) HELIX 1 AA1 SER A 14 LEU A 46 1 33 HELIX 2 AA2 ASP A 49 LEU A 74 1 26 HELIX 3 AA3 ASP A 79 GLU A 100 1 22 HELIX 4 AA4 LYS A 102 LEU A 112 1 11 HELIX 5 AA5 LEU A 112 ILE A 126 1 15 HELIX 6 AA6 PRO A 127 ALA A 129 5 3 HELIX 7 AA7 ASP A 130 HIS A 147 1 18 HELIX 8 AA8 ASN A 149 ASN A 158 1 10 HELIX 9 AA9 ASN A 158 LEU A 191 1 34 HELIX 10 AB1 GLU A 194 GLY A 214 1 21 HELIX 11 AB2 SER A 216 SER A 225 1 10 CRYST1 68.519 88.027 36.251 90.00 90.00 90.00 P 21 21 2 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 0.014594 0.000000 0.000000 0.00000 SCALE2 0.000000 0.011360 0.000000 0.00000 SCALE3 0.000000 0.000000 0.027585 0.00000