HEADER TRANSFERASE 05-JUL-19 6KEV TITLE REDUCED PHOSPHORIBULOKINASE FROM SYNECHOCOCCUS ELONGATUS PCC 7942 TITLE 2 COMPLEXED WITH ADENOSINE DIPHOSPHATE AND GLUCOSE 6-PHOSPHATE COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHORIBULOKINASE; COMPND 3 CHAIN: A; COMPND 4 EC: 2.7.1.19; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNECHOCOCCUS ELONGATUS (STRAIN PCC 7942); SOURCE 3 ORGANISM_TAXID: 1140; SOURCE 4 STRAIN: PCC 7942; SOURCE 5 GENE: SYNPCC7942_0977; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PHOSPHORIBULOKINASE, ADENOSINE DIPHOSPHATE, GLUCOSE 6-PHOSPHATE, KEYWDS 2 TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR A.YU,Y.XIE,M.LI REVDAT 3 29-JUL-20 6KEV 1 COMPND REMARK HETNAM SITE REVDAT 2 20-MAY-20 6KEV 1 JRNL REVDAT 1 13-MAY-20 6KEV 0 JRNL AUTH A.YU,Y.XIE,X.PAN,H.ZHANG,P.CAO,X.SU,W.CHANG,M.LI JRNL TITL PHOTOSYNTHETIC PHOSPHORIBULOKINASE STRUCTURES: ENZYMATIC JRNL TITL 2 MECHANISMS AND THE REDOX REGULATION OF THE JRNL TITL 3 CALVIN-BENSON-BASSHAM CYCLE. JRNL REF PLANT CELL V. 32 1556 2020 JRNL REFN ESSN 1532-298X JRNL PMID 32102842 JRNL DOI 10.1105/TPC.19.00642 REMARK 2 REMARK 2 RESOLUTION. 2.51 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.12_2829 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) : 2.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 29.14 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.344 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 12043 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.223 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.040 REMARK 3 FREE R VALUE TEST SET COUNT : 607 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 3.9757 - 3.1569 1.00 2874 146 0.1902 0.2291 REMARK 3 2 3.1569 - 2.7582 1.00 2829 148 0.2172 0.2650 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL 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) : 0.298 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 24.455 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.73 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.46 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 : 0.004 2645 REMARK 3 ANGLE : 0.732 3588 REMARK 3 CHIRALITY : 0.264 396 REMARK 3 PLANARITY : 0.004 460 REMARK 3 DIHEDRAL : 19.554 1010 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 6KEV COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 10-JUL-19. REMARK 100 THE DEPOSITION ID IS D_1300012831. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-NOV-15 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) : 0.98 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS3 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 12171 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 29.140 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 200 DATA REDUNDANCY : 12.20 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 18.4000 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) : NULL 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: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 47.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.34 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.02 M MAGNESIUM CHLORIDE HEXAHYDRATE, REMARK 280 0.05 M MES MONOHYDRATE PH6.0, 15% V/V 2-PROPANOL, 10MM ADENOSINE REMARK 280 DIPHOSPHATE, 10MM GLUCOSE 6-PHOSPHATE, VAPOR DIFFUSION, SITTING REMARK 280 DROP, TEMPERATURE 291.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 2 21 21 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,Y+1/2,-Z+1/2 REMARK 290 4555 -X,-Y+1/2,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 0.00000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 38.55200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 47.20250 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 38.55200 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 47.20250 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: 650 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 15100 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -4.0 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 MET A -1 REMARK 465 GLY A 0 REMARK 465 ARG A 144 REMARK 465 ASP A 145 REMARK 465 MET A 146 REMARK 465 ALA A 147 REMARK 465 GLU A 148 REMARK 465 ARG A 149 REMARK 465 GLY A 150 REMARK 465 HIS A 151 REMARK 465 ALA A 326 REMARK 465 ALA A 327 REMARK 465 PRO A 328 REMARK 465 VAL A 329 REMARK 465 ALA A 330 REMARK 465 ALA A 331 REMARK 465 SER A 332 REMARK 465 VAL A 333 REMARK 465 LEU A 334 REMARK 465 GLU A 335 REMARK 465 HIS A 336 REMARK 465 HIS A 337 REMARK 465 HIS A 338 REMARK 465 HIS A 339 REMARK 465 HIS A 340 REMARK 465 HIS A 341 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 ASN A 192 72.56 42.25 REMARK 500 PHE A 218 -70.68 64.52 REMARK 500 REMARK 500 REMARK: NULL DBREF 6KEV A 1 333 UNP Q31PL2 Q31PL2_SYNE7 1 333 SEQADV 6KEV MET A -1 UNP Q31PL2 EXPRESSION TAG SEQADV 6KEV GLY A 0 UNP Q31PL2 EXPRESSION TAG SEQADV 6KEV LEU A 334 UNP Q31PL2 EXPRESSION TAG SEQADV 6KEV GLU A 335 UNP Q31PL2 EXPRESSION TAG SEQADV 6KEV HIS A 336 UNP Q31PL2 EXPRESSION TAG SEQADV 6KEV HIS A 337 UNP Q31PL2 EXPRESSION TAG SEQADV 6KEV HIS A 338 UNP Q31PL2 EXPRESSION TAG SEQADV 6KEV HIS A 339 UNP Q31PL2 EXPRESSION TAG SEQADV 6KEV HIS A 340 UNP Q31PL2 EXPRESSION TAG SEQADV 6KEV HIS A 341 UNP Q31PL2 EXPRESSION TAG SEQRES 1 A 343 MET GLY MET SER LYS PRO ASP ARG VAL VAL LEU ILE GLY SEQRES 2 A 343 VAL ALA GLY ASP SER GLY CYS GLY LYS SER THR PHE LEU SEQRES 3 A 343 ASN ARG LEU ALA ASP LEU PHE GLY THR GLU LEU MET THR SEQRES 4 A 343 VAL ILE CYS LEU ASP ASP TYR HIS SER LEU ASP ARG LYS SEQRES 5 A 343 GLY ARG LYS GLU ALA GLY VAL THR ALA LEU ASP PRO ARG SEQRES 6 A 343 ALA ASN ASN PHE ASP LEU MET TYR GLU GLN VAL LYS ALA SEQRES 7 A 343 LEU LYS ASN GLY GLU THR ILE MET LYS PRO ILE TYR ASN SEQRES 8 A 343 HIS GLU THR GLY LEU ILE ASP PRO PRO GLU LYS ILE GLU SEQRES 9 A 343 PRO ASN ARG ILE ILE VAL ILE GLU GLY LEU HIS PRO LEU SEQRES 10 A 343 TYR ASP GLU ARG VAL ARG GLU LEU LEU ASP PHE SER VAL SEQRES 11 A 343 TYR LEU ASP ILE ASP ASP GLU VAL LYS ILE ALA TRP LYS SEQRES 12 A 343 ILE GLN ARG ASP MET ALA GLU ARG GLY HIS SER TYR GLU SEQRES 13 A 343 ASP VAL LEU ALA SER ILE GLU ALA ARG ARG PRO ASP PHE SEQRES 14 A 343 LYS ALA TYR ILE GLU PRO GLN ARG GLY HIS ALA ASP ILE SEQRES 15 A 343 VAL ILE ARG VAL MET PRO THR GLN LEU ILE PRO ASN ASP SEQRES 16 A 343 THR GLU ARG LYS VAL LEU ARG VAL GLN LEU ILE GLN ARG SEQRES 17 A 343 GLU GLY ARG ASP GLY PHE GLU PRO ALA TYR LEU PHE ASP SEQRES 18 A 343 GLU GLY SER THR ILE GLN TRP THR PRO CYS GLY ARG LYS SEQRES 19 A 343 LEU THR CYS SER TYR PRO GLY ILE ARG LEU ALA TYR GLY SEQRES 20 A 343 PRO ASP THR TYR TYR GLY HIS GLU VAL SER VAL LEU GLU SEQRES 21 A 343 VAL ASP GLY GLN PHE GLU ASN LEU GLU GLU MET ILE TYR SEQRES 22 A 343 VAL GLU GLY HIS LEU SER LYS THR ASP THR GLN TYR TYR SEQRES 23 A 343 GLY GLU LEU THR HIS LEU LEU LEU GLN HIS LYS ASP TYR SEQRES 24 A 343 PRO GLY SER ASN ASN GLY THR GLY LEU PHE GLN VAL LEU SEQRES 25 A 343 THR GLY LEU LYS MET ARG ALA ALA TYR GLU ARG LEU THR SEQRES 26 A 343 SER GLN ALA ALA PRO VAL ALA ALA SER VAL LEU GLU HIS SEQRES 27 A 343 HIS HIS HIS HIS HIS HET ADP A 401 27 HET G6P A 402 16 HET DTT A 403 8 HETNAM ADP ADENOSINE-5'-DIPHOSPHATE HETNAM G6P 6-O-PHOSPHONO-ALPHA-D-GLUCOPYRANOSE HETNAM DTT 2,3-DIHYDROXY-1,4-DITHIOBUTANE HETSYN DTT 1,4-DITHIOTHREITOL FORMUL 2 ADP C10 H15 N5 O10 P2 FORMUL 3 G6P C6 H13 O9 P FORMUL 4 DTT C4 H10 O2 S2 FORMUL 5 HOH *60(H2 O) HELIX 1 AA1 GLY A 19 GLY A 32 1 14 HELIX 2 AA2 ASP A 42 HIS A 45 5 4 HELIX 3 AA3 ASP A 48 GLY A 56 1 9 HELIX 4 AA4 ASP A 61 ASN A 65 5 5 HELIX 5 AA5 ASN A 66 ASN A 79 1 14 HELIX 6 AA6 ASP A 117 GLU A 122 1 6 HELIX 7 AA7 ASP A 133 GLN A 143 1 11 HELIX 8 AA8 TYR A 153 ILE A 171 1 19 HELIX 9 AA9 GLU A 172 ALA A 178 5 7 HELIX 10 AB1 ASN A 265 HIS A 275 1 11 HELIX 11 AB2 GLY A 285 GLN A 293 1 9 HELIX 12 AB3 ASN A 302 THR A 323 1 22 SHEET 1 AA1 9 MET A 36 CYS A 40 0 SHEET 2 AA1 9 ILE A 106 GLY A 111 1 O VAL A 108 N ILE A 39 SHEET 3 AA1 9 VAL A 8 ALA A 13 1 N ILE A 10 O ILE A 107 SHEET 4 AA1 9 PHE A 126 ILE A 132 1 O LEU A 130 N ALA A 13 SHEET 5 AA1 9 ILE A 180 PRO A 186 1 O VAL A 184 N ASP A 131 SHEET 6 AA1 9 LEU A 199 ARG A 206 -1 O ILE A 204 N VAL A 181 SHEET 7 AA1 9 HIS A 252 ASP A 260 -1 O LEU A 257 N LEU A 203 SHEET 8 AA1 9 ARG A 241 TYR A 249 -1 N ASP A 247 O VAL A 254 SHEET 9 AA1 9 ILE A 224 TRP A 226 -1 N TRP A 226 O LEU A 242 SHEET 1 AA2 2 ILE A 83 TYR A 88 0 SHEET 2 AA2 2 ILE A 95 ILE A 101 -1 O GLU A 99 N LYS A 85 SHEET 1 AA3 2 TYR A 216 LEU A 217 0 SHEET 2 AA3 2 LEU A 276 SER A 277 -1 O SER A 277 N TYR A 216 SSBOND 1 CYS A 229 CYS A 235 1555 1555 2.05 CISPEP 1 TYR A 237 PRO A 238 0 7.01 CRYST1 46.415 77.104 94.405 90.00 90.00 90.00 P 2 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 0.021545 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012969 0.000000 0.00000 SCALE3 0.000000 0.000000 0.010593 0.00000