HEADER METAL BINDING PROTEIN 06-NOV-22 8F23 TITLE THE CRYSTAL STRUCTURE OF A RATIONALLY DESIGNED ZINC SENSOR BASED ON TITLE 2 MALTOSE BINDING PROTEIN - APO CONFORMATION COMPND MOL_ID: 1; COMPND 2 MOLECULE: ZINC SENSOR PROTEIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MALTOSE/MALTODEXTRIN-BINDING PERIPLASMIC PROTEIN,MMBP, COMPND 5 MALTODEXTRIN-BINDING PROTEIN,MALTOSE-BINDING PROTEIN,MBP; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI; SOURCE 3 ORGANISM_TAXID: 562; SOURCE 4 GENE: MALE, Z5632, ECS5017; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008 KEYWDS ZINC, SENSING, XE NMR, METAL BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR Z.ZHAO,M.ZHOU,S.D.ZEMEROV,R.MARMORSTEIN,I.J.DMOCHOWSKI REVDAT 2 19-APR-23 8F23 1 JRNL REVDAT 1 22-MAR-23 8F23 0 JRNL AUTH Z.ZHAO,M.ZHOU,S.D.ZEMEROV,R.MARMORSTEIN,I.J.DMOCHOWSKI JRNL TITL RATIONAL DESIGN OF A GENETICALLY ENCODED NMR ZINC SENSOR. JRNL REF CHEM SCI V. 14 3809 2023 JRNL REFN ISSN 2041-6520 JRNL PMID 37035699 JRNL DOI 10.1039/D3SC00437F REMARK 2 REMARK 2 RESOLUTION. 1.93 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.20.1_4487 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.93 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 56.62 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.350 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 3 NUMBER OF REFLECTIONS : 24764 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.192 REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.229 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 8.060 REMARK 3 FREE R VALUE TEST SET COUNT : 1997 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 56.6200 - 4.6600 0.98 1677 148 0.1700 0.1854 REMARK 3 2 4.6600 - 3.7000 0.99 1655 144 0.1452 0.1863 REMARK 3 3 3.7000 - 3.2300 0.99 1650 145 0.1766 0.2199 REMARK 3 4 3.2300 - 2.9400 0.99 1641 144 0.1933 0.2195 REMARK 3 5 2.9400 - 2.7300 1.00 1640 143 0.2032 0.2885 REMARK 3 6 2.7300 - 2.5700 1.00 1650 145 0.1996 0.2729 REMARK 3 7 2.5700 - 2.4400 0.99 1636 144 0.2232 0.2829 REMARK 3 8 2.4400 - 2.3300 0.99 1646 144 0.2285 0.3010 REMARK 3 9 2.3300 - 2.2400 0.99 1636 144 0.2437 0.3276 REMARK 3 10 2.2400 - 2.1600 0.99 1637 143 0.2483 0.2763 REMARK 3 11 2.1600 - 2.1000 0.99 1610 143 0.2530 0.3254 REMARK 3 12 2.1000 - 2.0400 0.98 1609 139 0.2986 0.3457 REMARK 3 13 2.0400 - 1.9800 0.99 1618 143 0.3152 0.3242 REMARK 3 14 1.9800 - 1.9300 0.89 1462 128 0.3888 0.4346 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL REMARK 3 SOLVENT RADIUS : 1.10 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) : 0.299 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 31.119 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 42.90 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 61.49 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 2917 REMARK 3 ANGLE : 1.070 3964 REMARK 3 CHIRALITY : 0.066 430 REMARK 3 PLANARITY : 0.008 517 REMARK 3 DIHEDRAL : 15.993 1067 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 8F23 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 08-NOV-22. REMARK 100 THE DEPOSITION ID IS D_1000268460. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-MAR-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.0 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-C 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 EIGER2 X 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XDS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25254 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.920 REMARK 200 RESOLUTION RANGE LOW (A) : 68.430 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.1 REMARK 200 DATA REDUNDANCY : 6.800 REMARK 200 R MERGE (I) : 0.09900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 10.4000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.92 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.97 REMARK 200 COMPLETENESS FOR SHELL (%) : 77.3 REMARK 200 DATA REDUNDANCY IN SHELL : 5.90 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: PHASER REMARK 200 STARTING MODEL: 1OMP REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 42.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.12 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M SODIUM FORMATE, PH 7.0, 20% PEG REMARK 280 3350, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 34.21550 REMARK 290 SMTRY3 2 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 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 HIS A 111 ND1 CD2 CE1 NE2 REMARK 470 LYS A 127 CG CD CE NZ 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 ASP A 55 -162.10 -114.55 REMARK 500 LEU A 122 87.63 -152.48 REMARK 500 ALA A 168 -89.86 -80.36 REMARK 500 ASP A 209 -167.44 -107.79 REMARK 500 LYS A 256 76.71 -115.54 REMARK 500 GLN A 365 5.37 -64.11 REMARK 500 REMARK 500 REMARK: NULL DBREF 8F23 A 1 366 UNP P0AEY0 MALE_ECO57 27 392 SEQADV 8F23 HIS A 15 UNP P0AEY0 LYS 41 CONFLICT SEQADV 8F23 HIS A 111 UNP P0AEY0 GLU 137 CONFLICT SEQADV 8F23 HIS A 230 UNP P0AEY0 TRP 256 CONFLICT SEQRES 1 A 366 LYS ILE GLU GLU GLY LYS LEU VAL ILE TRP ILE ASN GLY SEQRES 2 A 366 ASP HIS GLY TYR ASN GLY LEU ALA GLU VAL GLY LYS LYS SEQRES 3 A 366 PHE GLU LYS ASP THR GLY ILE LYS VAL THR VAL GLU HIS SEQRES 4 A 366 PRO ASP LYS LEU GLU GLU LYS PHE PRO GLN VAL ALA ALA SEQRES 5 A 366 THR GLY ASP GLY PRO ASP ILE ILE PHE TRP ALA HIS ASP SEQRES 6 A 366 ARG PHE GLY GLY TYR ALA GLN SER GLY LEU LEU ALA GLU SEQRES 7 A 366 ILE THR PRO ASP LYS ALA PHE GLN ASP LYS LEU TYR PRO SEQRES 8 A 366 PHE THR TRP ASP ALA VAL ARG TYR ASN GLY LYS LEU ILE SEQRES 9 A 366 ALA TYR PRO ILE ALA VAL HIS ALA LEU SER LEU ILE TYR SEQRES 10 A 366 ASN LYS ASP LEU LEU PRO ASN PRO PRO LYS THR TRP GLU SEQRES 11 A 366 GLU ILE PRO ALA LEU ASP LYS GLU LEU LYS ALA LYS GLY SEQRES 12 A 366 LYS SER ALA LEU MET PHE ASN LEU GLN GLU PRO TYR PHE SEQRES 13 A 366 THR TRP PRO LEU ILE ALA ALA ASP GLY GLY TYR ALA PHE SEQRES 14 A 366 LYS TYR GLU ASN GLY LYS TYR ASP ILE LYS ASP VAL GLY SEQRES 15 A 366 VAL ASP ASN ALA GLY ALA LYS ALA GLY LEU THR PHE LEU SEQRES 16 A 366 VAL ASP LEU ILE LYS ASN LYS HIS MET ASN ALA ASP THR SEQRES 17 A 366 ASP TYR SER ILE ALA GLU ALA ALA PHE ASN LYS GLY GLU SEQRES 18 A 366 THR ALA MET THR ILE ASN GLY PRO HIS ALA TRP SER ASN SEQRES 19 A 366 ILE ASP THR SER LYS VAL ASN TYR GLY VAL THR VAL LEU SEQRES 20 A 366 PRO THR PHE LYS GLY GLN PRO SER LYS PRO PHE VAL GLY SEQRES 21 A 366 VAL LEU SER ALA GLY ILE ASN ALA ALA SER PRO ASN LYS SEQRES 22 A 366 GLU LEU ALA LYS GLU PHE LEU GLU ASN TYR LEU LEU THR SEQRES 23 A 366 ASP GLU GLY LEU GLU ALA VAL ASN LYS ASP LYS PRO LEU SEQRES 24 A 366 GLY ALA VAL ALA LEU LYS SER TYR GLU GLU GLU LEU ALA SEQRES 25 A 366 LYS ASP PRO ARG ILE ALA ALA THR MET GLU ASN ALA GLN SEQRES 26 A 366 LYS GLY GLU ILE MET PRO ASN ILE PRO GLN MET SER ALA SEQRES 27 A 366 PHE TRP TYR ALA VAL ARG THR ALA VAL ILE ASN ALA ALA SEQRES 28 A 366 SER GLY ARG GLN THR VAL ASP GLU ALA LEU LYS ASP ALA SEQRES 29 A 366 GLN THR FORMUL 2 HOH *72(H2 O) HELIX 1 AA1 GLY A 16 GLY A 32 1 17 HELIX 2 AA2 LYS A 42 ALA A 52 1 11 HELIX 3 AA3 HIS A 64 SER A 73 1 10 HELIX 4 AA4 ASP A 82 ASP A 87 1 6 HELIX 5 AA5 TYR A 90 ALA A 96 1 7 HELIX 6 AA6 THR A 128 GLU A 130 5 3 HELIX 7 AA7 GLU A 131 ALA A 141 1 11 HELIX 8 AA8 GLU A 153 ASP A 164 1 12 HELIX 9 AA9 ASN A 185 ASN A 201 1 17 HELIX 10 AB1 ASP A 209 LYS A 219 1 11 HELIX 11 AB2 GLY A 228 HIS A 230 5 3 HELIX 12 AB3 ALA A 231 SER A 238 1 8 HELIX 13 AB4 ASN A 272 TYR A 283 1 12 HELIX 14 AB5 THR A 286 LYS A 297 1 12 HELIX 15 AB6 LEU A 304 ALA A 312 1 9 HELIX 16 AB7 ASP A 314 GLY A 327 1 14 HELIX 17 AB8 GLN A 335 SER A 352 1 18 HELIX 18 AB9 THR A 356 GLN A 365 1 10 SHEET 1 AA1 6 LYS A 34 GLU A 38 0 SHEET 2 AA1 6 LYS A 6 TRP A 10 1 N ILE A 9 O THR A 36 SHEET 3 AA1 6 ILE A 59 ALA A 63 1 O PHE A 61 N TRP A 10 SHEET 4 AA1 6 PHE A 258 ILE A 266 -1 O GLY A 265 N ILE A 60 SHEET 5 AA1 6 TYR A 106 HIS A 111 -1 N ILE A 108 O LEU A 262 SHEET 6 AA1 6 ALA A 301 VAL A 302 -1 O ALA A 301 N VAL A 110 SHEET 1 AA2 5 LYS A 34 GLU A 38 0 SHEET 2 AA2 5 LYS A 6 TRP A 10 1 N ILE A 9 O THR A 36 SHEET 3 AA2 5 ILE A 59 ALA A 63 1 O PHE A 61 N TRP A 10 SHEET 4 AA2 5 PHE A 258 ILE A 266 -1 O GLY A 265 N ILE A 60 SHEET 5 AA2 5 GLU A 328 ILE A 329 1 O GLU A 328 N VAL A 259 SHEET 1 AA3 2 ARG A 98 TYR A 99 0 SHEET 2 AA3 2 LYS A 102 LEU A 103 -1 O LYS A 102 N TYR A 99 SHEET 1 AA4 3 MET A 224 ASN A 227 0 SHEET 2 AA4 3 SER A 114 ASN A 118 -1 N ILE A 116 O THR A 225 SHEET 3 AA4 3 TYR A 242 THR A 245 -1 O GLY A 243 N TYR A 117 SHEET 1 AA5 2 TYR A 167 TYR A 171 0 SHEET 2 AA5 2 TYR A 176 GLY A 182 -1 O ASP A 177 N LYS A 170 CRYST1 44.050 68.431 57.676 90.00 101.00 90.00 P 1 21 1 2 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 0.022701 0.000000 0.004413 0.00000 SCALE2 0.000000 0.014613 0.000000 0.00000 SCALE3 0.000000 0.000000 0.017663 0.00000