HEADER METAL BINDING PROTEIN 01-OCT-21 7PVC TITLE THE STRUCTURE OF KBP.K FROM E. COLI WITH POTASSIUM BOUND. COMPND MOL_ID: 1; COMPND 2 MOLECULE: POTASSIUM BINDING PROTEIN KBP; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: K(+) BINDING PROTEIN KBP; COMPND 5 ENGINEERED: YES; COMPND 6 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI (STRAIN K12); SOURCE 3 ORGANISM_TAXID: 83333; SOURCE 4 STRAIN: K12; SOURCE 5 GENE: KBP, YGAU, YZZM, B2665, JW2640; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PKA1 KEYWDS POTASSIUM ION BINDING METAL ION BINDING RESPONSE TO POTASSIUM ION KEYWDS 2 RESPONSE TO STIMULUS CYTOPLASM, METAL BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR B.O.SMITH REVDAT 7 11-OCT-23 7PVC 1 REMARK REVDAT 6 15-JUN-22 7PVC 1 JRNL REVDAT 5 08-JUN-22 7PVC 1 JRNL REVDAT 4 04-MAY-22 7PVC 1 JRNL REVDAT 3 16-FEB-22 7PVC 1 TITLE REVDAT 2 29-DEC-21 7PVC 1 KEYWDS REVDAT 1 13-OCT-21 7PVC 0 SPRSDE 13-OCT-21 7PVC 5FIM JRNL AUTH C.C.TORRES CABAN,M.YANG,C.LAI,L.YANG,F.V.SUBACH,B.O.SMITH, JRNL AUTH 2 K.D.PIATKEVICH,E.S.BOYDEN JRNL TITL TUNING THE SENSITIVITY OF GENETICALLY ENCODED FLUORESCENT JRNL TITL 2 POTASSIUM INDICATORS THROUGH STRUCTURE-GUIDED AND GENOME JRNL TITL 3 MINING STRATEGIES. JRNL REF ACS SENS V. 7 1336 2022 JRNL REFN ISSN 2379-3694 JRNL PMID 35427452 JRNL DOI 10.1021/ACSSENSORS.1C02201 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.U.ASHRAF,I.JOSTS,K.MOSBAHI,S.M.KELLY,O.BYRON,B.O.SMITH, REMARK 1 AUTH 2 D.WALKER REMARK 1 TITL THE POTASSIUM BINDING PROTEIN KBP IS A CYTOPLASMIC POTASSIUM REMARK 1 TITL 2 SENSOR. REMARK 1 REF STRUCTURE V. 24 741 2016 REMARK 1 REFN ISSN 1878-4186 REMARK 1 PMID 27112601 REMARK 1 DOI 10.1016/J.STR.2016.03.017 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : ARIA 2.3, CNS REMARK 3 AUTHORS : LINGE, O'DONOGHUE AND NILGES (ARIA), BRUNGER, REMARK 3 ADAMS, CLORE, GROS, NILGES AND READ (CNS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7PVC COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 01-OCT-21. REMARK 100 THE DEPOSITION ID IS D_1292117503. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 25 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1.5 MM [U-13C; U-15N] KBP, 20 MM REMARK 210 SODIUM PHOSPHATE, 5 MM POTASSIUM REMARK 210 CHLORIDE, 0.01 % SODIUM AZIDE, REMARK 210 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-13C HSQC; 3D CBCA(CO)NH; REMARK 210 3D 1H-13C NOESY; 2D HBCBCGHD; 2D REMARK 210 HBCBCGHE; 3D HBHA(CO)NH; 3D REMARK 210 HBHANH; 3D H(CCO)NH; 3D HCCH- REMARK 210 TOCSY; 3D HNCACB; 3D HNCACO; 3D REMARK 210 HNCO; 3D (H)C(CCO)NH; 2D 1H-15N REMARK 210 HSQC; 3D 1H-15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR ANALYSIS 2 REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : STRUCTURES WITH THE LEAST REMARK 210 RESTRAINT VIOLATIONS REMARK 210 REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 1 REMARK 210 REMARK 210 REMARK: NULL REMARK 215 REMARK 215 NMR STUDY REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION REMARK 215 NMR DATA. PROTEIN DATA BANK CONVENTIONS REQUIRE THAT REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON REMARK 215 THESE RECORDS ARE MEANINGLESS. 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: 0 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8320 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: 0.0 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 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS 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 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 RES CSSEQI ATM2 DEVIATION REMARK 500 1 TYR A 115 CE1 TYR A 115 CZ -0.090 REMARK 500 9 TYR A 115 CE1 TYR A 115 CZ -0.079 REMARK 500 13 TYR A 115 CE1 TYR A 115 CZ -0.116 REMARK 500 13 TYR A 115 CZ TYR A 115 CE2 0.104 REMARK 500 19 PHE A 125 CE1 PHE A 125 CZ 0.131 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 1 GLN A 21 -83.38 68.74 REMARK 500 1 HIS A 22 -72.82 -136.07 REMARK 500 1 VAL A 46 -169.24 -104.66 REMARK 500 1 ASP A 52 -72.03 68.17 REMARK 500 1 ASN A 76 46.10 -107.57 REMARK 500 1 PRO A 140 108.64 -53.93 REMARK 500 1 GLU A 151 88.73 54.39 REMARK 500 1 HIS A 154 -155.68 62.61 REMARK 500 1 HIS A 155 -70.63 67.79 REMARK 500 2 ASP A 16 104.48 64.63 REMARK 500 2 GLN A 21 -76.52 72.27 REMARK 500 2 HIS A 22 -41.02 -174.54 REMARK 500 2 ALA A 51 69.35 -111.50 REMARK 500 2 ASP A 52 -71.53 69.16 REMARK 500 2 PRO A 140 109.70 -53.35 REMARK 500 2 HIS A 154 -78.16 -79.87 REMARK 500 2 HIS A 155 -174.20 57.19 REMARK 500 2 HIS A 156 -30.92 -167.18 REMARK 500 3 VAL A 18 -58.73 -124.10 REMARK 500 3 GLN A 21 131.90 73.67 REMARK 500 3 ASP A 42 18.47 57.47 REMARK 500 3 ASP A 52 -67.50 71.14 REMARK 500 3 ASN A 76 41.78 -107.39 REMARK 500 3 ALA A 90 -43.58 67.65 REMARK 500 3 LYS A 137 32.51 -93.31 REMARK 500 3 PRO A 140 108.76 -51.77 REMARK 500 3 GLU A 151 -23.58 74.20 REMARK 500 3 HIS A 152 -115.38 58.91 REMARK 500 3 HIS A 156 128.36 71.10 REMARK 500 4 ASP A 16 -7.79 65.41 REMARK 500 4 VAL A 18 -78.19 -120.19 REMARK 500 4 ASP A 52 -67.65 69.63 REMARK 500 4 PRO A 140 103.95 -55.67 REMARK 500 4 LEU A 150 47.78 -80.19 REMARK 500 4 GLU A 151 111.25 63.77 REMARK 500 4 HIS A 153 -175.87 67.40 REMARK 500 4 HIS A 154 167.03 68.34 REMARK 500 5 PHE A 6 -169.70 -127.32 REMARK 500 5 LYS A 8 -62.77 -105.31 REMARK 500 5 TRP A 15 -81.61 -143.04 REMARK 500 5 ASP A 16 -78.25 168.54 REMARK 500 5 LYS A 24 -71.50 -142.63 REMARK 500 5 ASP A 42 18.22 57.10 REMARK 500 5 ASP A 52 -62.72 73.49 REMARK 500 5 ASN A 76 57.91 -102.04 REMARK 500 5 PRO A 140 107.20 -56.04 REMARK 500 5 LEU A 150 90.52 -68.93 REMARK 500 5 GLU A 151 -176.67 59.42 REMARK 500 6 ASP A 16 103.14 66.96 REMARK 500 6 GLN A 21 90.40 62.54 REMARK 500 REMARK 500 THIS ENTRY HAS 192 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 15 TYR A 121 0.05 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 K A 201 K REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL A 7 O REMARK 620 2 ALA A 10 O 118.3 REMARK 620 3 GLY A 75 O 97.3 127.4 REMARK 620 4 ILE A 77 O 124.4 71.4 119.9 REMARK 620 5 ILE A 80 O 56.3 129.2 102.3 75.3 REMARK 620 N 1 2 3 4 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 5FIM RELATED DB: PDB REMARK 900 STRUCTURE DETERMINED BEFORE K+ BINDING SITE IDENTIFIED REMARK 900 RELATED ID: 25839 RELATED DB: BMRB DBREF 7PVC A 1 149 UNP P0ADE6 KBP_ECOLI 1 149 SEQADV 7PVC LEU A 150 UNP P0ADE6 EXPRESSION TAG SEQADV 7PVC GLU A 151 UNP P0ADE6 EXPRESSION TAG SEQADV 7PVC HIS A 152 UNP P0ADE6 EXPRESSION TAG SEQADV 7PVC HIS A 153 UNP P0ADE6 EXPRESSION TAG SEQADV 7PVC HIS A 154 UNP P0ADE6 EXPRESSION TAG SEQADV 7PVC HIS A 155 UNP P0ADE6 EXPRESSION TAG SEQADV 7PVC HIS A 156 UNP P0ADE6 EXPRESSION TAG SEQADV 7PVC HIS A 157 UNP P0ADE6 EXPRESSION TAG SEQRES 1 A 157 MET GLY LEU PHE ASN PHE VAL LYS ASP ALA GLY GLU LYS SEQRES 2 A 157 LEU TRP ASP ALA VAL THR GLY GLN HIS ASP LYS ASP ASP SEQRES 3 A 157 GLN ALA LYS LYS VAL GLN GLU HIS LEU ASN LYS THR GLY SEQRES 4 A 157 ILE PRO ASP ALA ASP LYS VAL ASN ILE GLN ILE ALA ASP SEQRES 5 A 157 GLY LYS ALA THR VAL THR GLY ASP GLY LEU SER GLN GLU SEQRES 6 A 157 ALA LYS GLU LYS ILE LEU VAL ALA VAL GLY ASN ILE SER SEQRES 7 A 157 GLY ILE ALA SER VAL ASP ASP GLN VAL LYS THR ALA THR SEQRES 8 A 157 PRO ALA THR ALA SER GLN PHE TYR THR VAL LYS SER GLY SEQRES 9 A 157 ASP THR LEU SER ALA ILE SER LYS GLN VAL TYR GLY ASN SEQRES 10 A 157 ALA ASN LEU TYR ASN LYS ILE PHE GLU ALA ASN LYS PRO SEQRES 11 A 157 MET LEU LYS SER PRO ASP LYS ILE TYR PRO GLY GLN VAL SEQRES 12 A 157 LEU ARG ILE PRO GLU GLU LEU GLU HIS HIS HIS HIS HIS SEQRES 13 A 157 HIS HET K A 201 1 HETNAM K POTASSIUM ION FORMUL 2 K K 1+ HELIX 1 AA1 ASP A 23 GLY A 39 1 17 HELIX 2 AA2 GLN A 64 ASN A 76 1 13 HELIX 3 AA3 THR A 106 TYR A 115 1 10 HELIX 4 AA4 ASN A 117 ASN A 119 5 3 HELIX 5 AA5 LEU A 120 LYS A 129 1 10 HELIX 6 AA6 SER A 134 ILE A 138 5 5 SHEET 1 AA1 4 LEU A 3 ASN A 5 0 SHEET 2 AA1 4 SER A 82 THR A 91 -1 O VAL A 83 N PHE A 4 SHEET 3 AA1 4 LYS A 54 SER A 63 1 N GLY A 59 O LYS A 88 SHEET 4 AA1 4 VAL A 46 ALA A 51 -1 N GLN A 49 O THR A 56 SHEET 1 AA2 2 GLN A 97 THR A 100 0 SHEET 2 AA2 2 VAL A 143 ILE A 146 -1 O ILE A 146 N GLN A 97 LINK O VAL A 7 K K A 201 1555 1555 2.68 LINK O ALA A 10 K K A 201 1555 1555 2.63 LINK O GLY A 75 K K A 201 1555 1555 2.61 LINK O ILE A 77 K K A 201 1555 1555 2.70 LINK O ILE A 80 K K A 201 1555 1555 2.66 CISPEP 1 LYS A 129 PRO A 130 1 -7.58 CISPEP 2 LYS A 129 PRO A 130 2 0.04 CISPEP 3 LYS A 129 PRO A 130 3 -7.60 CISPEP 4 LYS A 129 PRO A 130 4 -5.82 CISPEP 5 LYS A 129 PRO A 130 5 -7.58 CISPEP 6 LYS A 129 PRO A 130 6 -6.85 CISPEP 7 LYS A 129 PRO A 130 7 -3.82 CISPEP 8 LYS A 129 PRO A 130 8 -9.71 CISPEP 9 LYS A 129 PRO A 130 9 -5.70 CISPEP 10 LYS A 129 PRO A 130 10 6.93 CISPEP 11 LYS A 129 PRO A 130 11 -6.27 CISPEP 12 LYS A 129 PRO A 130 12 -10.11 CISPEP 13 LYS A 129 PRO A 130 13 -7.58 CISPEP 14 LYS A 129 PRO A 130 14 -5.29 CISPEP 15 LYS A 129 PRO A 130 15 7.54 CISPEP 16 LYS A 129 PRO A 130 16 -6.93 CISPEP 17 LYS A 129 PRO A 130 17 -8.00 CISPEP 18 LYS A 129 PRO A 130 18 -8.47 CISPEP 19 LYS A 129 PRO A 130 19 7.23 CISPEP 20 LYS A 129 PRO A 130 20 -6.45 CRYST1 1.000 1.000 1.000 90.00 90.00 90.00 P 1 1 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 1.000000 0.000000 0.000000 0.00000 SCALE2 0.000000 1.000000 0.000000 0.00000 SCALE3 0.000000 0.000000 1.000000 0.00000 MODEL 1