HEADER PLANT PROTEIN 05-SEP-19 6KVN TITLE CRYSTAL STRUCTURE OF CHLOROPLAST RESOLVASE COMPND MOL_ID: 1; COMPND 2 MOLECULE: NTMOC1; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES; COMPND 5 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: NICOTIANA TABACUM; SOURCE 3 ORGANISM_COMMON: COMMON TOBACCO; SOURCE 4 ORGANISM_TAXID: 4097; SOURCE 5 GENE: LOC107823122; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3) KEYWDS CHLOROPLAST, RESOLVASE, PLANT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.J.YAN,S.X.HONG,Z.Y.GUAN,P.YIN REVDAT 2 27-MAR-24 6KVN 1 REMARK REVDAT 1 08-APR-20 6KVN 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. 2.02 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.14RC3_3206 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 : CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.02 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 43.57 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.360 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.6 REMARK 3 NUMBER OF REFLECTIONS : 10508 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.194 REMARK 3 R VALUE (WORKING SET) : 0.192 REMARK 3 FREE R VALUE : 0.237 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.390 REMARK 3 FREE R VALUE TEST SET COUNT : 566 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 43.5700 - 3.2100 1.00 2618 132 0.1770 0.2109 REMARK 3 2 3.2100 - 2.5500 1.00 2477 151 0.2038 0.2715 REMARK 3 3 2.5500 - 2.2200 1.00 2429 153 0.2080 0.2418 REMARK 3 4 2.2200 - 2.0200 0.99 2418 130 0.2124 0.2618 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) : 0.227 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.863 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 29.46 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.33 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 1185 REMARK 3 ANGLE : 0.774 1607 REMARK 3 CHIRALITY : 0.055 174 REMARK 3 PLANARITY : 0.007 202 REMARK 3 DIHEDRAL : 20.846 427 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): -10.2845 11.2042 -16.4450 REMARK 3 T TENSOR REMARK 3 T11: 0.1792 T22: 0.1779 REMARK 3 T33: 0.1646 T12: 0.0132 REMARK 3 T13: 0.0376 T23: -0.0173 REMARK 3 L TENSOR REMARK 3 L11: 2.6477 L22: 3.0900 REMARK 3 L33: 1.1304 L12: 0.1349 REMARK 3 L13: 0.2690 L23: -0.5733 REMARK 3 S TENSOR REMARK 3 S11: -0.0042 S12: -0.2337 S13: 0.1755 REMARK 3 S21: 0.3622 S22: -0.0210 S23: 0.3711 REMARK 3 S31: -0.1631 S32: -0.2246 S33: 0.0230 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 6KVN COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 05-SEP-19. REMARK 100 THE DEPOSITION ID IS D_1300013729. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 13-JUN-19 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 : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97918 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10538 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.020 REMARK 200 RESOLUTION RANGE LOW (A) : 43.570 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : 0.20700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 6.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.02 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.07 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : 0.85300 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.600 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: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.27 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.06 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: BIS-TRIS, PEG 3350, LITHIUM SULPHAT, REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 291.15K 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 31.39650 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 20.16750 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 31.39650 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 20.16750 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1800 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 16390 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -19.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 1.000000 0.00000 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 A 334 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 A 105 REMARK 465 HIS A 106 REMARK 465 MET A 107 REMARK 465 ASN A 108 REMARK 465 LEU A 143 REMARK 465 VAL A 144 REMARK 465 GLY A 145 REMARK 465 LYS A 146 REMARK 465 GLY A 147 REMARK 465 VAL A 148 REMARK 465 ARG A 149 REMARK 465 THR A 224 REMARK 465 LYS A 225 REMARK 465 GLU A 226 REMARK 465 ARG A 227 REMARK 465 SER A 228 REMARK 465 ASN A 229 REMARK 465 LYS A 230 REMARK 465 SER A 273 REMARK 465 ASP A 274 REMARK 465 SER A 275 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 353 O HOH A 358 1.84 REMARK 500 O HOH A 312 O HOH A 357 1.88 REMARK 500 O HOH A 344 O HOH A 354 1.97 REMARK 500 O HOH A 333 O HOH A 360 2.02 REMARK 500 O HOH A 302 O HOH A 355 2.11 REMARK 500 OE1 GLN A 176 O HOH A 301 2.13 REMARK 500 O HOH A 305 O HOH A 317 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 SER A 120 36.20 -99.79 REMARK 500 GLN A 182 51.73 -96.78 REMARK 500 REMARK 500 REMARK: NULL DBREF1 6KVN A 108 275 UNP A0A1S4CVP6_TOBAC DBREF2 6KVN A A0A1S4CVP6 108 275 SEQADV 6KVN ALA A 105 UNP A0A1S4CVP EXPRESSION TAG SEQADV 6KVN HIS A 106 UNP A0A1S4CVP EXPRESSION TAG SEQADV 6KVN MET A 107 UNP A0A1S4CVP EXPRESSION TAG SEQADV 6KVN LYS A 162 UNP A0A1S4CVP GLN 162 ENGINEERED MUTATION SEQADV 6KVN GLN A 235 UNP A0A1S4CVP GLU 235 ENGINEERED MUTATION SEQADV 6KVN GLN A 239 UNP A0A1S4CVP GLU 239 ENGINEERED MUTATION SEQRES 1 A 171 ALA HIS MET ASN ALA GLY TRP VAL ILE GLY VAL ASP PRO SEQRES 2 A 171 ASP THR SER GLY ALA LEU ALA LEU LEU LYS PRO ASN GLN SEQRES 3 A 171 PRO PRO GLN VAL PHE ASP SER PRO HIS LEU LYS VAL LEU SEQRES 4 A 171 VAL GLY LYS GLY VAL ARG LYS ARG LEU ASP ALA LYS ALA SEQRES 5 A 171 ILE VAL GLN LEU LEU LYS SER PHE GLU ALA PRO ILE GLY SEQRES 6 A 171 THR THR VAL TYR VAL GLU GLN SER THR PRO TYR PRO GLN SEQRES 7 A 171 ASP GLY LYS GLN GLY TRP TRP SER GLY GLY PHE GLY TYR SEQRES 8 A 171 GLY MET TRP ILE GLY ILE LEU VAL ALA SER GLY PHE SER SEQRES 9 A 171 VAL ILE PRO VAL PRO SER SER ALA TRP LYS SER GLU PHE SEQRES 10 A 171 GLN LEU THR LYS GLU ARG SER ASN LYS ASP TYR SER ARG SEQRES 11 A 171 GLN VAL ALA SER GLN LEU PHE PRO SER LEU SER SER LEU SEQRES 12 A 171 LEU LYS ARG LYS LYS ASP HIS GLY ARG ALA GLU ALA LEU SEQRES 13 A 171 LEU ILE ALA ALA TYR GLY LYS GLY ILE LYS ILE ASN SER SEQRES 14 A 171 ASP SER FORMUL 2 HOH *61(H2 O) HELIX 1 AA1 ASP A 153 PHE A 164 1 12 HELIX 2 AA2 GLY A 184 SER A 205 1 22 HELIX 3 AA3 PRO A 213 PHE A 221 1 9 HELIX 4 AA4 TYR A 232 PHE A 241 1 10 HELIX 5 AA5 PRO A 242 LYS A 249 5 8 HELIX 6 AA6 ARG A 250 LYS A 252 5 3 HELIX 7 AA7 ASP A 253 GLY A 268 1 16 SHEET 1 AA1 5 GLN A 133 ASP A 136 0 SHEET 2 AA1 5 ALA A 122 LEU A 126 -1 N LEU A 123 O PHE A 135 SHEET 3 AA1 5 VAL A 112 ASP A 116 -1 N VAL A 112 O LEU A 126 SHEET 4 AA1 5 THR A 171 GLU A 175 1 O TYR A 173 N ILE A 113 SHEET 5 AA1 5 SER A 208 VAL A 212 1 O SER A 208 N VAL A 172 CRYST1 62.793 40.335 60.504 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 0.015925 0.000000 0.000000 0.00000 SCALE2 0.000000 0.024792 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016528 0.00000