HEADER DE NOVO PROTEIN 09-JAN-18 6C2V TITLE SOLUTION STRUCTURE OF A PHOSPHATE-LOOP PROTEIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: PHOSPHATE-LOOP PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SYNTHETIC CONSTRUCT; SOURCE 3 ORGANISM_TAXID: 32630; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS PROTEIN DESIGN, PHOSPHATE LOOP, IDEAL FOLD, GRAFTING, DE NOVO PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR F.YANG,W.YANG,Y.R.LIN,M.L.ROMERO ROMERO,D.TAWFIK,D.BAKER,G.VARANI REVDAT 7 15-MAY-24 6C2V 1 REMARK REVDAT 6 14-JUN-23 6C2V 1 REMARK REVDAT 5 17-APR-19 6C2V 1 REMARK REVDAT 4 02-JAN-19 6C2V 1 JRNL REVDAT 3 19-DEC-18 6C2V 1 JRNL REVDAT 2 28-NOV-18 6C2V 1 JRNL REVDAT 1 21-NOV-18 6C2V 0 JRNL AUTH M.L.ROMERO ROMERO,F.YANG,Y.R.LIN,A.TOTH-PETROCZY, JRNL AUTH 2 I.N.BEREZOVSKY,A.GONCEARENCO,W.YANG,A.WELLNER, JRNL AUTH 3 F.KUMAR-DESHMUKH,M.SHARON,D.BAKER,G.VARANI,D.S.TAWFIK JRNL TITL SIMPLE YET FUNCTIONAL PHOSPHATE-LOOP PROTEINS. JRNL REF PROC. NATL. ACAD. SCI. V. 115 11943 2018 JRNL REF 2 U.S.A. JRNL REFN ESSN 1091-6490 JRNL PMID 30504143 JRNL DOI 10.1073/PNAS.1812400115 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : AMBER REMARK 3 AUTHORS : CASE, DARDEN, CHEATHAM III, SIMMERLING, WANG, REMARK 3 DUKE, LUO, ... AND KOLLMAN REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6C2V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 22-JAN-18. REMARK 100 THE DEPOSITION ID IS D_1000231985. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.0 REMARK 210 IONIC STRENGTH : 50 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 2 MM [U-13C; U-15N] PROTEIN, 10 REMARK 210 MM SODIUM PHOSPHATE, 50 MM REMARK 210 SODIUM CHLORIDE, 90% H2O/10% D2O; REMARK 210 1 MM [U-15N] PROTEIN, 10 MM REMARK 210 SODIUM PHOSPHATE, 50 MM SODIUM REMARK 210 CHLORIDE, 90% H2O/10% D2O; 2 MM REMARK 210 [U-13C; U-15N] PROTEIN, 10 MM REMARK 210 SODIUM PHOSPHATE, 50 MM SODIUM REMARK 210 CHLORIDE, 100% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 2D 1H-13C HSQC; REMARK 210 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 HNCO; 3D HBHA(CO)NH; 3D HCCH- REMARK 210 TOCSY; 3D 1H-15N NOESY; 3D 1H- REMARK 210 13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : CCPNMR, TOPSPIN, NMRPIPE, CYANA, REMARK 210 TALOS 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 LOWEST REMARK 210 ENERGY 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 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: COVALENT BOND ANGLES 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,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) 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 ATM2 ATM3 REMARK 500 1 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 1 ARG A 103 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 ARG A 2 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 2 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 ARG A 53 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 ARG A 103 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 5 ARG A 2 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 ARG A 35 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 5 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 ARG A 2 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 6 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 6 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 7 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 7 ARG A 103 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 8 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 4.3 DEGREES REMARK 500 8 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 9 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 9 ARG A 52 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 11 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 11 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 12 ARG A 2 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 12 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 12 ARG A 45 NE - CZ - NH2 ANGL. DEV. = -3.0 DEGREES REMARK 500 13 ARG A 2 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 13 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 14 ARG A 2 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 14 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 14 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 14 ARG A 81 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 15 ARG A 2 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 15 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 15 ARG A 52 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 16 ARG A 2 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 16 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 17 ARG A 2 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 17 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 4.6 DEGREES REMARK 500 17 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 18 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 18 ARG A 53 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 19 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 19 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 20 ARG A 23 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 20 ARG A 35 NE - CZ - NH1 ANGL. DEV. = 3.6 DEGREES REMARK 500 20 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 20 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 51 ANGLE DEVIATIONS. 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 ASN A 54 64.94 63.71 REMARK 500 1 ALA A 55 92.69 -60.81 REMARK 500 1 PRO A 63 -71.75 -74.29 REMARK 500 1 SER A 66 -35.29 -156.11 REMARK 500 1 ALA A 102 -54.10 -141.51 REMARK 500 1 HIS A 113 4.82 -66.97 REMARK 500 2 ASN A 54 62.40 66.57 REMARK 500 2 ALA A 55 92.82 -59.83 REMARK 500 2 PRO A 63 -84.69 -69.01 REMARK 500 2 SER A 64 -47.82 -179.85 REMARK 500 2 SER A 69 3.24 -64.19 REMARK 500 2 THR A 91 37.33 -81.26 REMARK 500 2 ALA A 102 -55.72 -138.93 REMARK 500 3 ASN A 54 61.33 65.61 REMARK 500 3 ALA A 55 92.62 -59.51 REMARK 500 3 SER A 64 -9.09 -146.56 REMARK 500 3 LYS A 68 -6.92 -147.97 REMARK 500 3 SER A 69 44.84 -75.75 REMARK 500 3 GLU A 93 -29.48 -164.77 REMARK 500 3 ALA A 102 -54.07 -139.84 REMARK 500 3 HIS A 113 -87.05 49.39 REMARK 500 3 HIS A 114 -41.19 -165.81 REMARK 500 4 LYS A 15 -80.93 -119.86 REMARK 500 4 ALA A 55 88.85 -62.96 REMARK 500 4 SER A 64 -31.07 -165.38 REMARK 500 4 SER A 69 9.52 -65.60 REMARK 500 4 THR A 91 30.35 -71.67 REMARK 500 4 ALA A 102 -53.40 -142.49 REMARK 500 5 LYS A 15 -51.76 -134.80 REMARK 500 5 ASN A 54 61.92 65.28 REMARK 500 5 ALA A 55 90.80 -60.49 REMARK 500 5 LYS A 68 -3.10 -59.05 REMARK 500 5 SER A 69 4.92 -59.63 REMARK 500 5 GLU A 92 -44.88 -163.44 REMARK 500 5 ALA A 102 -52.87 -142.38 REMARK 500 5 HIS A 113 -33.82 -162.11 REMARK 500 6 ASN A 54 65.59 64.01 REMARK 500 6 ALA A 55 92.65 -61.92 REMARK 500 6 PRO A 63 -81.35 -64.53 REMARK 500 6 SER A 64 156.98 163.74 REMARK 500 6 THR A 91 28.27 -73.26 REMARK 500 6 ALA A 102 -54.18 -141.91 REMARK 500 6 HIS A 110 40.77 -81.88 REMARK 500 6 HIS A 112 -149.87 -149.41 REMARK 500 6 HIS A 113 -2.99 -50.12 REMARK 500 6 HIS A 114 37.76 -77.06 REMARK 500 7 ALA A 13 -42.70 59.18 REMARK 500 7 ASN A 54 62.19 60.23 REMARK 500 7 ALA A 55 90.13 -60.77 REMARK 500 7 PRO A 63 -76.59 -70.95 REMARK 500 REMARK 500 THIS ENTRY HAS 157 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 6C2U RELATED DB: PDB REMARK 900 RELATED ID: 30395 RELATED DB: BMRB REMARK 900 SOLUTION STRUCTURE OF A PHOSPHATE-LOOP PROTEIN DBREF 6C2V A 1 115 PDB 6C2V 6C2V 1 115 SEQRES 1 A 115 MET ARG VAL ILE VAL VAL ILE VAL GLY PRO SER GLY ALA SEQRES 2 A 115 GLY LYS THR THR LEU ASP GLU LEU ALA ARG LYS ALA LYS SEQRES 3 A 115 GLU GLU VAL PRO ASP ALA GLU ILE ARG THR VAL THR THR SEQRES 4 A 115 LYS GLU ASP ALA LYS ARG VAL ALA GLU GLU ALA GLU ARG SEQRES 5 A 115 ARG ASN ALA ASP ILE VAL VAL ILE VAL GLY PRO SER GLY SEQRES 6 A 115 SER GLY LYS SER THR LEU ALA LYS ILE VAL LYS LYS ILE SEQRES 7 A 115 ILE ALA ARG ALA GLY ALA LYS THR ILE GLU VAL THR THR SEQRES 8 A 115 GLU GLU GLU LEU ARG LYS ALA VAL ALA LYS ALA ARG GLY SEQRES 9 A 115 SER TRP SER LEU GLU HIS HIS HIS HIS HIS HIS HELIX 1 AA1 THR A 16 VAL A 29 1 14 HELIX 2 AA2 THR A 39 ASN A 54 1 16 HELIX 3 AA3 SER A 69 GLY A 83 1 15 HELIX 4 AA4 GLU A 94 LYS A 101 1 8 HELIX 5 AA5 GLY A 104 HIS A 111 1 8 SHEET 1 AA1 4 GLU A 33 VAL A 37 0 SHEET 2 AA1 4 VAL A 3 VAL A 8 1 N ILE A 7 O VAL A 37 SHEET 3 AA1 4 ILE A 57 VAL A 61 1 O VAL A 59 N ILE A 4 SHEET 4 AA1 4 LYS A 85 GLU A 88 1 O ILE A 87 N ILE A 60 CISPEP 1 GLY A 9 PRO A 10 1 5.48 CISPEP 2 GLY A 9 PRO A 10 2 -8.14 CISPEP 3 GLY A 9 PRO A 10 3 12.62 CISPEP 4 GLY A 9 PRO A 10 4 -13.95 CISPEP 5 GLY A 9 PRO A 10 5 6.78 CISPEP 6 GLY A 9 PRO A 10 6 5.58 CISPEP 7 GLY A 9 PRO A 10 7 4.45 CISPEP 8 GLY A 9 PRO A 10 8 0.04 CISPEP 9 GLY A 9 PRO A 10 9 -1.07 CISPEP 10 GLY A 9 PRO A 10 10 -2.07 CISPEP 11 GLY A 9 PRO A 10 11 12.09 CISPEP 12 GLY A 9 PRO A 10 12 -10.04 CISPEP 13 GLY A 9 PRO A 10 13 8.68 CISPEP 14 GLY A 9 PRO A 10 14 -12.56 CISPEP 15 GLY A 9 PRO A 10 15 8.29 CISPEP 16 GLY A 9 PRO A 10 16 9.97 CISPEP 17 GLY A 9 PRO A 10 17 6.16 CISPEP 18 GLY A 9 PRO A 10 18 -10.09 CISPEP 19 GLY A 9 PRO A 10 19 -5.23 CISPEP 20 GLY A 9 PRO A 10 20 12.06 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