HEADER PLANT PROTEIN 06-APR-18 6G7G TITLE STRUCTURE OF SPH (SELF-INCOMPATIBILITY PROTEIN HOMOLOGUE) PROTEINS, A TITLE 2 WIDESPREAD FAMILY OF SMALL, HIGHLY STABLE, SECRETED PROTEINS FROM TITLE 3 PLANTS COMPND MOL_ID: 1; COMPND 2 MOLECULE: S-PROTEIN HOMOLOG 15; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ARABIDOPSIS THALIANA; SOURCE 3 ORGANISM_COMMON: MOUSE-EAR CRESS; SOURCE 4 ORGANISM_TAXID: 3702; SOURCE 5 GENE: SPH15, AT5G39493, MUL8.19; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SELF-INCOMPATIBILITY PROTEIN HOMOLOG, ORIGAMI STRAIN E COLI, PLANT KEYWDS 2 PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR K.V.RAJASEKAR,R.J.COULTHARD,J.P.RIDE,S.JI,P.J.WINN,M.P.WHEELER, AUTHOR 2 E.I.HYDE,L.J.SMITH REVDAT 5 13-NOV-24 6G7G 1 REMARK REVDAT 4 14-JUN-23 6G7G 1 REMARK REVDAT 3 08-MAY-19 6G7G 1 REMARK REVDAT 2 20-MAR-19 6G7G 1 JRNL REVDAT 1 06-MAR-19 6G7G 0 JRNL AUTH K.V.RAJASEKAR,S.JI,R.J.COULTHARD,J.P.RIDE,G.L.REYNOLDS, JRNL AUTH 2 P.J.WINN,M.J.WHEELER,E.I.HYDE,L.J.SMITH JRNL TITL STRUCTURE OF SPH (SELF-INCOMPATIBILITY PROTEIN HOMOLOGUE) JRNL TITL 2 PROTEINS: A WIDESPREAD FAMILY OF SMALL, HIGHLY STABLE, JRNL TITL 3 SECRETED PROTEINS. JRNL REF BIOCHEM.J. V. 476 809 2019 JRNL REFN ESSN 1470-8728 JRNL PMID 30782970 JRNL DOI 10.1042/BCJ20180828 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS REMARK 3 AUTHORS : BRUNGER A. T. ET.AL. REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6G7G COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 06-APR-18. REMARK 100 THE DEPOSITION ID IS D_1200009455. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 5.2 REMARK 210 IONIC STRENGTH : 0.01 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 0.3 MM [U-13C; U-15N] SPH15, 95% REMARK 210 H2O/5% D2O; 1 MM [U-13C; U-15N] REMARK 210 SPH15, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCACB; 3D HN(COCA)CB; 3D REMARK 210 HNCO; 3D HNCACO; 3D HBHA(CO)NH; REMARK 210 3D HCCH-COSY; 3D HCCH-TOCSY; 3D REMARK 210 1H-15N TOCSY; 3D 1H-15N NOESY; REMARK 210 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 500 MHZ; 800 MHZ; 600 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE; INOVA REMARK 210 SPECTROMETER MANUFACTURER : BRUKER; VARIAN REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : ARIA, CCPNMR ANALYSIS REMARK 210 METHOD USED : TORSION ANGLE DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 200 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 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: 6910 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 3 PHE A 61 CE1 PHE A 61 CZ 0.201 REMARK 500 3 PHE A 61 CZ PHE A 61 CE2 -0.178 REMARK 500 3 PHE A 70 CZ PHE A 70 CE2 0.135 REMARK 500 6 TYR A 76 CE1 TYR A 76 CZ 0.085 REMARK 500 6 TYR A 76 CZ TYR A 76 CE2 -0.091 REMARK 500 7 PHE A 61 CE1 PHE A 61 CZ 0.175 REMARK 500 7 PHE A 61 CZ PHE A 61 CE2 -0.124 REMARK 500 8 PHE A 61 CE1 PHE A 61 CZ 0.283 REMARK 500 8 PHE A 61 CZ PHE A 61 CE2 -0.217 REMARK 500 9 PHE A 47 CE1 PHE A 47 CZ 0.154 REMARK 500 9 PHE A 47 CZ PHE A 47 CE2 -0.130 REMARK 500 9 TYR A 76 CE1 TYR A 76 CZ -0.090 REMARK 500 9 TYR A 76 CZ TYR A 76 CE2 0.085 REMARK 500 10 TYR A 36 CE1 TYR A 36 CZ -0.140 REMARK 500 10 TYR A 36 CZ TYR A 36 CE2 0.149 REMARK 500 10 PHE A 61 CE1 PHE A 61 CZ 0.235 REMARK 500 10 PHE A 61 CZ PHE A 61 CE2 -0.185 REMARK 500 10 TYR A 76 CE1 TYR A 76 CZ -0.210 REMARK 500 10 TYR A 76 CZ TYR A 76 CE2 0.219 REMARK 500 11 PHE A 61 CE1 PHE A 61 CZ 0.191 REMARK 500 11 PHE A 61 CZ PHE A 61 CE2 -0.156 REMARK 500 12 PHE A 70 CZ PHE A 70 CE2 0.129 REMARK 500 13 PHE A 61 CE1 PHE A 61 CZ 0.211 REMARK 500 13 PHE A 61 CZ PHE A 61 CE2 -0.130 REMARK 500 14 PHE A 47 CZ PHE A 47 CE2 0.133 REMARK 500 15 TYR A 36 CE1 TYR A 36 CZ -0.129 REMARK 500 15 TYR A 36 CZ TYR A 36 CE2 0.145 REMARK 500 15 PHE A 61 CE1 PHE A 61 CZ 0.186 REMARK 500 15 PHE A 61 CZ PHE A 61 CE2 -0.121 REMARK 500 15 TYR A 99 CE1 TYR A 99 CZ 0.109 REMARK 500 15 TYR A 99 CZ TYR A 99 CE2 -0.119 REMARK 500 16 PHE A 70 CZ PHE A 70 CE2 0.118 REMARK 500 17 PHE A 70 CZ PHE A 70 CE2 0.122 REMARK 500 18 TYR A 23 CZ TYR A 23 CE2 0.113 REMARK 500 18 PHE A 70 CE1 PHE A 70 CZ 0.137 REMARK 500 20 PHE A 39 CE1 PHE A 39 CZ 0.126 REMARK 500 REMARK 500 REMARK: NULL 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 10 TYR A 76 OH - CZ - CE2 ANGL. DEV. = -18.6 DEGREES REMARK 500 10 TYR A 76 CZ - CE2 - CD2 ANGL. DEV. = -5.8 DEGREES 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 CYS A 4 -178.28 68.07 REMARK 500 1 THR A 14 85.89 179.61 REMARK 500 1 VAL A 32 -59.45 -128.40 REMARK 500 1 PHE A 39 98.58 -57.57 REMARK 500 1 LYS A 40 -63.59 -130.90 REMARK 500 1 ASP A 49 42.17 -75.28 REMARK 500 1 THR A 52 -130.43 -77.32 REMARK 500 1 SER A 55 9.34 -161.53 REMARK 500 1 ARG A 56 -153.81 36.14 REMARK 500 1 ILE A 65 -162.45 173.15 REMARK 500 1 ASN A 66 -167.08 -63.93 REMARK 500 1 LYS A 68 -95.95 30.11 REMARK 500 1 PRO A 78 35.58 -82.67 REMARK 500 1 LEU A 84 -117.51 -96.79 REMARK 500 1 CYS A 85 -86.01 64.23 REMARK 500 1 MET A 95 -47.29 -21.21 REMARK 500 1 ASP A 96 -76.80 -86.88 REMARK 500 1 ASP A 103 -168.97 -126.74 REMARK 500 2 THR A 14 88.95 -173.44 REMARK 500 2 LYS A 40 -60.69 -179.45 REMARK 500 2 ASP A 49 -161.46 57.19 REMARK 500 2 ASP A 50 75.05 50.98 REMARK 500 2 THR A 52 130.11 58.69 REMARK 500 2 SER A 55 -115.37 -167.72 REMARK 500 2 ARG A 56 -139.05 168.02 REMARK 500 2 ILE A 65 -83.69 -162.51 REMARK 500 2 ASN A 66 -152.10 -112.37 REMARK 500 2 THR A 71 149.59 -174.65 REMARK 500 2 PRO A 78 88.82 -50.18 REMARK 500 2 CYS A 85 -67.36 -146.55 REMARK 500 2 MET A 95 -66.67 49.59 REMARK 500 2 MET A 102 93.13 -53.18 REMARK 500 2 GLU A 104 -37.43 43.43 REMARK 500 2 PRO A 109 98.34 -60.36 REMARK 500 2 TRP A 113 152.98 -45.23 REMARK 500 3 VAL A 32 -65.88 -106.46 REMARK 500 3 ASP A 50 -92.65 -111.21 REMARK 500 3 ARG A 56 -152.36 38.69 REMARK 500 3 ASN A 66 -145.54 -55.93 REMARK 500 3 PHE A 69 104.95 -169.27 REMARK 500 3 THR A 71 144.90 170.01 REMARK 500 3 ARG A 77 88.25 -154.19 REMARK 500 3 CYS A 85 -11.72 -169.35 REMARK 500 3 MET A 95 -65.09 -12.67 REMARK 500 3 GLU A 104 -2.35 68.53 REMARK 500 3 ASN A 111 105.85 177.26 REMARK 500 3 TRP A 113 92.36 -68.03 REMARK 500 3 ARG A 114 -147.78 30.42 REMARK 500 4 CYS A 4 22.47 -174.64 REMARK 500 4 THR A 14 74.85 -158.09 REMARK 500 REMARK 500 THIS ENTRY HAS 399 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 MET A 102 ASP A 103 2 145.91 REMARK 500 ARG A 94 MET A 95 6 145.52 REMARK 500 LYS A 5 GLU A 6 9 147.99 REMARK 500 ASN A 66 MET A 67 11 149.02 REMARK 500 THR A 14 LEU A 15 14 147.62 REMARK 500 PRO A 78 ASP A 79 15 148.11 REMARK 500 ASN A 66 MET A 67 17 149.13 REMARK 500 GLY A 86 LYS A 87 20 -148.20 REMARK 500 LYS A 87 ARG A 88 20 -144.34 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 6 TYR A 76 0.05 SIDE CHAIN REMARK 500 7 PHE A 61 0.06 SIDE CHAIN REMARK 500 8 PHE A 61 0.08 SIDE CHAIN REMARK 500 10 TYR A 76 0.07 SIDE CHAIN REMARK 500 13 PHE A 61 0.09 SIDE CHAIN REMARK 500 15 TYR A 36 0.06 SIDE CHAIN REMARK 500 15 PHE A 61 0.08 SIDE CHAIN REMARK 500 18 TYR A 23 0.09 SIDE CHAIN REMARK 500 18 PHE A 39 0.08 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 27439 RELATED DB: BMRB DBREF 6G7G A 4 115 UNP Q9FLY6 SPH15_ARATH 21 132 SEQADV 6G7G ALA A 1 UNP Q9FLY6 EXPRESSION TAG SEQADV 6G7G MET A 2 UNP Q9FLY6 EXPRESSION TAG SEQADV 6G7G GLY A 3 UNP Q9FLY6 EXPRESSION TAG SEQRES 1 A 115 ALA MET GLY CYS LYS GLU ILE GLU ILE VAL ILE LYS ASN SEQRES 2 A 115 THR LEU GLY PRO SER ARG ILE LEU GLN TYR HIS CYS ARG SEQRES 3 A 115 SER GLY ASN THR ASN VAL GLY VAL GLN TYR LEU ASN PHE SEQRES 4 A 115 LYS GLY THR ARG ILE ILE LYS PHE LYS ASP ASP GLY THR SEQRES 5 A 115 GLU ARG SER ARG TRP ASN CYS LEU PHE ARG GLN GLY ILE SEQRES 6 A 115 ASN MET LYS PHE PHE THR GLU VAL GLU ALA TYR ARG PRO SEQRES 7 A 115 ASP LEU LYS HIS PRO LEU CYS GLY LYS ARG TYR GLU LEU SEQRES 8 A 115 SER ALA ARG MET ASP ALA ILE TYR PHE LYS MET ASP GLU SEQRES 9 A 115 ARG PRO PRO GLN PRO LEU ASN LYS TRP ARG SER SHEET 1 AA1 3 THR A 42 LYS A 46 0 SHEET 2 AA1 3 GLU A 8 THR A 14 -1 N ILE A 9 O ILE A 45 SHEET 3 AA1 3 GLU A 90 ARG A 94 1 O ALA A 93 N THR A 14 SHEET 1 AA2 4 VAL A 34 ASN A 38 0 SHEET 2 AA2 4 ILE A 20 ARG A 26 -1 N TYR A 23 O GLN A 35 SHEET 3 AA2 4 ASN A 58 ARG A 62 -1 O ARG A 62 N GLN A 22 SHEET 4 AA2 4 THR A 71 GLU A 74 -1 O VAL A 73 N CYS A 59 SHEET 1 AA3 2 ILE A 98 TYR A 99 0 SHEET 2 AA3 2 PRO A 109 ASN A 111 -1 O ASN A 111 N ILE A 98 SSBOND 1 CYS A 4 CYS A 85 1555 1555 2.03 SSBOND 2 CYS A 25 CYS A 59 1555 1555 2.04 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