HEADER HYDROLASE 19-NOV-19 6LCM TITLE CRYSTAL STRUCTURE OF CHLOROPLAST RESOLVASE ZMMOC1 WITH THE MAGIC TITLE 2 TRIANGLE I3C COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZMMOC1; COMPND 3 CHAIN: C; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ZEA MAYS; SOURCE 3 ORGANISM_COMMON: MAIZE; SOURCE 4 ORGANISM_TAXID: 4577; SOURCE 5 GENE: 100192759, ZEAMMB73_ZM00001D040409; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS CHLOROPLAST, RESOLVASE, HOLLIDAY JUNCTION, PLANT PROTEIN, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR J.J.YAN,S.X.HONG,Z.Y.GUAN,P.YIN REVDAT 2 27-MAR-24 6LCM 1 REMARK REVDAT 1 08-APR-20 6LCM 0 JRNL AUTH J.YAN,S.HONG,Z.GUAN,W.HE,D.ZHANG,P.YIN JRNL TITL STRUCTURAL INSIGHTS INTO SEQUENCE-DEPENDENT HOLLIDAY JRNL TITL 2 JUNCTION RESOLUTION BY THE CHLOROPLAST RESOLVASE MOC1. JRNL REF NAT COMMUN V. 11 1417 2020 JRNL REFN ESSN 2041-1723 JRNL PMID 32184398 JRNL DOI 10.1038/S41467-020-15242-8 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX V1.5 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) : 45.00 REMARK 3 MIN(FOBS/SIGMA_FOBS) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 6519 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.223 REMARK 3 FREE R VALUE : 0.280 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.260 REMARK 3 FREE R VALUE TEST SET COUNT : 343 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : NULL REMARK 3 SHRINKAGE RADIUS : NULL REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : NULL REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 29.72 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 : 0.006 1345 REMARK 3 ANGLE : 0.684 1832 REMARK 3 CHIRALITY : 0.055 195 REMARK 3 PLANARITY : 0.003 230 REMARK 3 DIHEDRAL : 14.575 768 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 6LCM COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 20-NOV-19. REMARK 100 THE DEPOSITION ID IS D_1300014474. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-SEP-17 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU MICROMAX-007 HF REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 R 200K-A REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6571 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 45.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 33.80 REMARK 200 R MERGE (I) : 0.09200 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 70.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.30200 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: SAD REMARK 200 SOFTWARE USED: SHELXDE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.16 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.24 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, AMMONIUM FLUORIDE, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 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+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 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 70.91550 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 24.56800 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 24.56800 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 106.37325 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 24.56800 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 24.56800 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 35.45775 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 24.56800 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 24.56800 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 106.37325 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 24.56800 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 24.56800 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 35.45775 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 70.91550 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 2710 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16300 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -18.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C 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 350 BIOMT1 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 141.83100 REMARK 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH C 324 LIES ON A SPECIAL POSITION. 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 ALA C -2 REMARK 465 HIS C -1 REMARK 465 MET C 0 REMARK 465 THR C 1 REMARK 465 ASN C 2 REMARK 465 PHE C 73 REMARK 465 SER C 170 REMARK 465 LYS C 171 REMARK 465 THR C 172 REMARK 465 SER C 173 REMARK 465 VAL C 174 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 C 352 O HOH C 353 1.87 REMARK 500 N PRO C 74 O HOH C 301 1.93 REMARK 500 O HOH C 306 O HOH C 349 2.04 REMARK 500 I2 I3C C 202 O HOH C 329 2.07 REMARK 500 OD1 ASP C 76 O HOH C 302 2.09 REMARK 500 OD2 ASP C 136 O HOH C 303 2.12 REMARK 500 N GLU C 39 O HOH C 304 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 ARG C 118 58.03 -115.47 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 I3C C 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue I3C C 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: binding site for residue I3C C 203 DBREF 6LCM C 1 174 UNP B4FCI7 B4FCI7_MAIZE 107 280 SEQADV 6LCM ALA C -2 UNP B4FCI7 EXPRESSION TAG SEQADV 6LCM HIS C -1 UNP B4FCI7 EXPRESSION TAG SEQADV 6LCM MET C 0 UNP B4FCI7 EXPRESSION TAG SEQADV 6LCM GLU C 52 UNP B4FCI7 GLN 158 ENGINEERED MUTATION SEQADV 6LCM VAL C 105 UNP B4FCI7 ILE 211 ENGINEERED MUTATION SEQRES 1 C 177 ALA HIS MET THR ASN GLY TRP VAL ILE GLY VAL ASP PRO SEQRES 2 C 177 ASP ILE GLY GLY ALA ILE ALA VAL LEU SER PRO ASP GLY SEQRES 3 C 177 SER SER GLN VAL PHE ASP ASN PRO PHE VAL HIS ILE VAL SEQRES 4 C 177 VAL SER GLU VAL ILE ARG LYS ARG LEU ASP THR LYS SER SEQRES 5 C 177 ILE ILE GLU LEU LEU ARG GLY LEU ASP ALA PRO PRO GLY SEQRES 6 C 177 THR THR ALA TYR ILE GLU LYS SER SER PRO PHE PRO THR SEQRES 7 C 177 ASP GLY LYS GLN GLY TRP TRP SER THR GLY PHE SER TYR SEQRES 8 C 177 GLY LEU TRP ILE ALA SER LEU VAL ALA SER GLY PHE SER SEQRES 9 C 177 VAL VAL PRO VAL ALA SER GLN THR TRP LYS ALA TYR PHE SEQRES 10 C 177 GLY LEU MET ARG SER GLU THR PRO LYS ASP ASP SER ARG SEQRES 11 C 177 GLN ALA ALA SER ILE LEU PHE PRO ASP LYS ASP GLN SER SEQRES 12 C 177 LEU LYS LEU LYS LYS HIS HIS GLY ARG ALA GLU ALA LEU SEQRES 13 C 177 LEU LEU ALA ALA TYR GLY LYS GLY LEU VAL LEU PRO SER SEQRES 14 C 177 GLY LYS PHE SER LYS THR SER VAL HET I3C C 201 16 HET I3C C 202 16 HET I3C C 203 16 HETNAM I3C 5-AMINO-2,4,6-TRIIODOBENZENE-1,3-DICARBOXYLIC ACID HETSYN I3C 5-AMINO-2,4,6-TRIIODOISOPHTHALIC ACID FORMUL 2 I3C 3(C8 H4 I3 N O4) FORMUL 5 HOH *53(H2 O) HELIX 1 AA1 ASP C 46 GLY C 56 1 11 HELIX 2 AA2 GLY C 80 SER C 98 1 19 HELIX 3 AA3 SER C 107 PHE C 114 1 8 HELIX 4 AA4 THR C 121 PHE C 134 1 14 HELIX 5 AA5 PRO C 135 LYS C 142 5 8 HELIX 6 AA6 LEU C 143 LYS C 145 5 3 HELIX 7 AA7 HIS C 146 GLY C 161 1 16 SHEET 1 AA1 5 SER C 25 ASP C 29 0 SHEET 2 AA1 5 ALA C 15 LEU C 19 -1 N ILE C 16 O PHE C 28 SHEET 3 AA1 5 VAL C 5 ASP C 9 -1 N GLY C 7 O ALA C 17 SHEET 4 AA1 5 THR C 64 LYS C 69 1 O TYR C 66 N ILE C 6 SHEET 5 AA1 5 SER C 101 ALA C 106 1 O SER C 101 N ALA C 65 SHEET 1 AA2 2 PHE C 32 VAL C 37 0 SHEET 2 AA2 2 VAL C 40 LEU C 45 -1 O ARG C 42 N ILE C 35 SITE 1 AC1 7 ASP C 124 ARG C 127 GLN C 128 SER C 131 SITE 2 AC1 7 ASP C 138 LEU C 141 LYS C 142 SITE 1 AC2 9 ASP C 46 THR C 47 VAL C 102 PRO C 104 SITE 2 AC2 9 ALA C 112 MET C 117 ARG C 118 HOH C 307 SITE 3 AC2 9 HOH C 329 SITE 1 AC3 6 VAL C 36 VAL C 37 LYS C 69 VAL C 105 SITE 2 AC3 6 ALA C 106 HOH C 317 CRYST1 49.136 49.136 141.831 90.00 90.00 90.00 P 43 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 0.020352 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020352 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007051 0.00000