HEADER MEMBRANE PROTEIN 13-MAR-19 6R0J TITLE THE N-TERMINAL DOMAIN OF RHOMBOID PROTEASE YQGP COMPND MOL_ID: 1; COMPND 2 MOLECULE: RHOMBOID FAMILY SERINE PROTEASE; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BACILLUS SUBTILIS; SOURCE 3 ORGANISM_TAXID: 1423; SOURCE 4 GENE: B4122_2383, B4122_4232, B4417_0943; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RHOMBOID PROTEASE, BACILLUS SUBTILIS, METAL BINDING, MEMBRANE PROTEIN EXPDTA SOLUTION NMR NUMMDL 30 AUTHOR J.BEGAN,K.STRISOVSKY,V.VEVERKA REVDAT 5 19-JUN-24 6R0J 1 REMARK REVDAT 4 14-JUN-23 6R0J 1 REMARK REVDAT 3 03-JUN-20 6R0J 1 JRNL REVDAT 2 22-JAN-20 6R0J 1 JRNL REVDAT 1 08-JAN-20 6R0J 0 JRNL AUTH J.BEGAN,B.CORDIER,J.BREZINOVA,J.DELISLE,R.HEXNEROVA,P.SRB, JRNL AUTH 2 P.RAMPIROVA,M.KOZISEK,M.BAUDET,Y.COUTE,A.GALINIER,V.VEVERKA, JRNL AUTH 3 T.DOAN,K.STRISOVSKY JRNL TITL RHOMBOID INTRAMEMBRANE PROTEASE YQGP LICENSES BACTERIAL JRNL TITL 2 MEMBRANE PROTEIN QUALITY CONTROL AS ADAPTOR OF FTSH AAA JRNL TITL 3 PROTEASE. JRNL REF EMBO J. V. 39 02935 2020 JRNL REFN ESSN 1460-2075 JRNL PMID 31930742 JRNL DOI 10.15252/EMBJ.2019102935 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : YASARA REMARK 3 AUTHORS : YASARA REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6R0J COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-MAR-19. REMARK 100 THE DEPOSITION ID IS D_1292101225. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 6.5 REMARK 210 IONIC STRENGTH : 175 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 1 MM [U-13C; U-15N] YQGP, 150 MM REMARK 210 SODIUM CHLORIDE, 25 MM SODIUM REMARK 210 PHOSPHATE, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 3D HNCACB; 3D CBCA(CO)NH; 3D REMARK 210 HNCO; 3D HCCH-TOCSY; 3D 1H-15N REMARK 210 NOESY; 3D 1H-13C NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 850 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN, CYANA, SPARKY REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 100 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 30 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 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: 11650 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: 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 4 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 5 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 ARG A 79 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 6 ARG A 133 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 11 ARG A 179 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 13 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 13 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 13 ARG A 165 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 14 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 16 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 16 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 17 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 17 ARG A 77 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 17 ARG A 122 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 19 ARG A 59 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 22 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 25 ARG A 45 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 26 ARG A 133 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 28 ARG A 72 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 29 ARG A 165 NE - CZ - NH1 ANGL. DEV. = 3.0 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 ASP A 95 6.28 47.22 REMARK 500 1 MET A 120 26.92 -140.94 REMARK 500 1 ASN A 181 -57.98 -152.35 REMARK 500 1 LEU A 182 -161.52 58.35 REMARK 500 2 PHE A 2 -51.31 -132.52 REMARK 500 2 SER A 28 -69.43 -158.40 REMARK 500 2 SER A 39 -177.66 -68.19 REMARK 500 2 ASP A 95 51.25 19.84 REMARK 500 2 ALA A 142 -44.73 63.25 REMARK 500 2 PHE A 172 -42.97 -158.91 REMARK 500 2 GLN A 173 -145.15 40.08 REMARK 500 3 SER A 40 -1.56 -54.20 REMARK 500 3 ASP A 95 9.24 48.40 REMARK 500 3 MET A 120 40.66 -147.58 REMARK 500 3 PHE A 184 150.80 67.57 REMARK 500 4 SER A 39 -177.68 -70.00 REMARK 500 4 ASP A 95 27.55 40.14 REMARK 500 4 GLN A 173 -56.09 64.30 REMARK 500 4 ASN A 181 119.86 60.61 REMARK 500 5 SER A 28 -73.24 -166.67 REMARK 500 5 SER A 39 -173.34 -63.61 REMARK 500 5 ASP A 95 19.48 45.88 REMARK 500 5 ALA A 142 34.85 -86.09 REMARK 500 5 LEU A 182 -160.05 61.97 REMARK 500 6 ASP A 95 70.98 14.88 REMARK 500 6 MET A 120 32.85 -140.56 REMARK 500 6 CYS A 137 116.44 -169.97 REMARK 500 6 LEU A 177 -97.43 -130.68 REMARK 500 7 PHE A 2 141.31 69.67 REMARK 500 7 SER A 28 -74.74 -154.37 REMARK 500 7 SER A 39 -172.96 -67.21 REMARK 500 7 ASP A 95 60.41 14.43 REMARK 500 7 MET A 120 36.52 -144.65 REMARK 500 7 ASN A 174 -119.92 64.79 REMARK 500 8 SER A 28 -75.12 -165.15 REMARK 500 8 SER A 39 -177.43 -62.57 REMARK 500 8 ASP A 94 56.21 -110.04 REMARK 500 8 MET A 120 35.83 -140.97 REMARK 500 9 ASP A 95 15.89 49.80 REMARK 500 9 MET A 120 25.44 -141.49 REMARK 500 9 CYS A 137 48.91 -92.84 REMARK 500 9 GLU A 180 91.17 40.84 REMARK 500 9 ASN A 181 39.11 -144.10 REMARK 500 10 SER A 39 -177.71 -69.73 REMARK 500 10 ASP A 95 28.66 44.52 REMARK 500 10 MET A 120 30.84 -140.60 REMARK 500 10 ALA A 142 40.96 -102.62 REMARK 500 10 GLU A 178 148.57 70.20 REMARK 500 10 GLU A 180 169.08 65.71 REMARK 500 10 PHE A 184 150.97 65.30 REMARK 500 REMARK 500 THIS ENTRY HAS 189 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34376 RELATED DB: BMRB REMARK 900 THE N-TERMINAL DOMAIN OF RHOMBOID PROTEASE YQGP DBREF1 6R0J A 1 176 UNP A0A162T8T3_BACIU DBREF2 6R0J A A0A162T8T3 1 176 SEQADV 6R0J LEU A 177 UNP A0A162T8T EXPRESSION TAG SEQADV 6R0J GLU A 178 UNP A0A162T8T EXPRESSION TAG SEQADV 6R0J ARG A 179 UNP A0A162T8T EXPRESSION TAG SEQADV 6R0J GLU A 180 UNP A0A162T8T EXPRESSION TAG SEQADV 6R0J ASN A 181 UNP A0A162T8T EXPRESSION TAG SEQADV 6R0J LEU A 182 UNP A0A162T8T EXPRESSION TAG SEQADV 6R0J TYR A 183 UNP A0A162T8T EXPRESSION TAG SEQADV 6R0J PHE A 184 UNP A0A162T8T EXPRESSION TAG SEQADV 6R0J GLN A 185 UNP A0A162T8T EXPRESSION TAG SEQRES 1 A 185 MET PHE LEU LEU GLU TYR THR TYR TRP LYS ILE ALA ALA SEQRES 2 A 185 HIS LEU VAL ASN SER GLY TYR GLY VAL ILE GLN ALA GLY SEQRES 3 A 185 GLU SER ASP GLU ILE TRP LEU GLU ALA PRO ASP LYS SER SEQRES 4 A 185 SER HIS ASP LEU VAL ARG LEU TYR LYS HIS ASP LEU ASP SEQRES 5 A 185 PHE ARG GLN GLU MET VAL ARG ASP ILE GLU GLU GLN ALA SEQRES 6 A 185 GLU ARG VAL GLU ARG VAL ARG HIS GLN LEU GLY ARG ARG SEQRES 7 A 185 ARG MET LYS LEU LEU ASN VAL PHE PHE SER THR GLU ALA SEQRES 8 A 185 PRO VAL ASP ASP TRP GLU GLU ILE ALA LYS LYS THR PHE SEQRES 9 A 185 GLU LYS GLY THR VAL SER VAL GLU PRO ALA ILE VAL ARG SEQRES 10 A 185 GLY THR MET LEU ARG ASP ASP LEU GLN ALA VAL PHE PRO SEQRES 11 A 185 SER PHE ARG THR GLU ASP CYS SER GLU GLU HIS ALA SER SEQRES 12 A 185 PHE GLU ASN ALA GLN MET ALA ARG GLU ARG PHE LEU SER SEQRES 13 A 185 LEU VAL LEU LYS GLN GLU GLU GLN ARG LYS THR GLU ALA SEQRES 14 A 185 ALA VAL PHE GLN ASN GLY LYS LEU GLU ARG GLU ASN LEU SEQRES 15 A 185 TYR PHE GLN HELIX 1 AA1 PHE A 2 ASN A 17 1 16 HELIX 2 AA2 PHE A 53 GLY A 76 1 24 HELIX 3 AA3 ASP A 95 LYS A 101 1 7 HELIX 4 AA4 MET A 120 PHE A 129 1 10 HELIX 5 AA5 ARG A 133 SER A 138 5 6 HELIX 6 AA6 GLU A 145 ALA A 169 1 25 SHEET 1 AA1 6 GLY A 21 GLN A 24 0 SHEET 2 AA1 6 GLU A 30 GLU A 34 -1 O GLU A 34 N GLY A 21 SHEET 3 AA1 6 LEU A 43 LYS A 48 -1 O VAL A 44 N LEU A 33 SHEET 4 AA1 6 MET A 80 SER A 88 1 O LEU A 83 N ARG A 45 SHEET 5 AA1 6 VAL A 109 ARG A 117 1 O VAL A 116 N PHE A 86 SHEET 6 AA1 6 PHE A 104 LYS A 106 -1 N PHE A 104 O VAL A 111 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