HEADER RNA BINDING PROTEIN 19-SEP-20 7AFQ TITLE RIBOSOME BINDING FACTOR A (RBFA) COMPND MOL_ID: 1; COMPND 2 MOLECULE: RIBOSOME-BINDING FACTOR A; COMPND 3 CHAIN: V; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ESCHERICHIA COLI O26:H11; SOURCE 3 ORGANISM_TAXID: 244319; SOURCE 4 GENE: RBFA, B9S25_002975; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS SOLUTION STATE NMR, 30S BIOGENESIS, RIBOSOME ASSEMBLY, RBFA., RNA KEYWDS 2 BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR A.SCHEDLBAUER,I.ITURRIOZ,B.OCHOA-LIZARRALDE,T.DIERCKS,P.FUCINI, AUTHOR 2 S.CONNELL REVDAT 6 14-JUN-23 7AFQ 1 REMARK REVDAT 5 08-DEC-21 7AFQ 1 REMARK REVDAT 4 16-JUN-21 7AFQ 1 JRNL REVDAT 3 17-MAR-21 7AFQ 1 OBSLTE SPRSDE REVDAT 2 10-MAR-21 7AFQ 1 OBSLTE REVDAT 1 16-DEC-20 7AFQ 0 SPRSDE 16-DEC-20 7AFQ 6R8D JRNL AUTH A.SCHEDLBAUER,I.ITURRIOZ,B.OCHOA-LIZARRALDE,T.DIERCKS, JRNL AUTH 2 J.P.LOPEZ-ALONSO,J.L.LAVIN,T.KAMINISHI,R.CAPUNI,N.DHIMOLE, JRNL AUTH 3 E.DE ASTIGARRAGA,D.GIL-CARTON,P.FUCINI,S.R.CONNELL JRNL TITL A CONSERVED RRNA SWITCH IS CENTRAL TO DECODING SITE JRNL TITL 2 MATURATION ON THE SMALL RIBOSOMAL SUBUNIT. JRNL REF SCI ADV V. 7 2021 JRNL REFN ESSN 2375-2548 JRNL PMID 34088665 JRNL DOI 10.1126/SCIADV.ABF7547 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR NIH, GROMACS REMARK 3 AUTHORS : SCHWIETERS, KUSZEWSKI, TJANDRA AND CLORE (X-PLOR REMARK 3 NIH), EMILE APOL, ROSSEN APOSTOLOV, PAUL BAUER, REMARK 3 HERMAN J.C. BERENDSEN, PAR BJELKMAR, CHRISTIAN REMARK 3 BLAU, VIACHESLAV BOLNYKH, KEVIN BOYD, ALDERT VAN REMARK 3 BUUREN, RUDI VAN DRUNEN, ANTON FEENSTRA, ALAN GRAY, REMARK 3 GERRIT GROENHOF, ANCA HAMURARU, VINCENT REMARK 3 HINDRIKSEN M. ERIC IRRGANG, ALEKSEI IUPINOV, REMARK 3 CHRISTOPH JUNGHANS, JOE JORDAN, DIMITRIOS REMARK 3 KARKOULIS, PETER KASSON,, JIRI KRAUS, CARSTEN REMARK 3 KUTZNER, PER LARSSON, JUSTIN A. LEMKUL, VIVECA REMARK 3 LINDAHL, MAGNUS LUNDBORG, ERIK MARKLUND, PASCAL REMARK 3 MERZ, PIETER MEULENHOFF, TEEMU MURTOLA, SZILARD REMARK 3 PALL, SANDER PRONK, ROLAND SCHULZ, MICHAEL SHIRTS, REMARK 3 ALEXEY SHVETSOV, ALFONS SIJBERS, PETER TIELEMAN, REMARK 3 JON VINCENT, TEEMU VIROLAINEN, CHRISTIAN WENNBERG, REMARK 3 MAARTEN WOLF, ARTEM ZHMUROV. (GROMACS) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7AFQ COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-SEP-20. REMARK 100 THE DEPOSITION ID IS D_1292110868. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 293 REMARK 210 PH : 7.6 REMARK 210 IONIC STRENGTH : 40 REMARK 210 PRESSURE : 1 ATM REMARK 210 SAMPLE CONTENTS : 400 UM [U-13C; U-15N] RBFA, 10 REMARK 210 MM HEPES, 6 MM MGCL2, 30 MM REMARK 210 NH4CL, 75 UM TCEP, 90% H2O/10% REMARK 210 D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D HNCO; 3D REMARK 210 HNCA; 3D HNCACB; 3D CBCA(CO)NH; REMARK 210 3D HN(CO)CA; 3D HNCAHA; 3D HCCH- REMARK 210 TOCSY; 3D HN(CA)CO; 3D HNH NOESY; REMARK 210 3D CNH NOESY; 3D HN(CO)CAHA; 3D REMARK 210 HCH NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 600 MHZ; 800 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE III REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : NMRPIPE, SPARKY, CCPNMR ANALYSIS REMARK 210 METHOD USED : SIMULATED ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 60 REMARK 210 CONFORMERS, NUMBER SUBMITTED : 20 REMARK 210 CONFORMERS, SELECTION CRITERIA : TARGET FUNCTION 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: V 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 465 REMARK 465 MISSING RESIDUES REMARK 465 THE FOLLOWING RESIDUES WERE NOT LOCATED IN THE REMARK 465 EXPERIMENT. (RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 465 SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 MODELS 1-20 REMARK 465 RES C SSSEQI REMARK 465 MET V 1 REMARK 465 ALA V 2 REMARK 465 LYS V 3 REMARK 465 GLU V 4 REMARK 465 PHE V 5 REMARK 465 GLY V 6 REMARK 465 ARG V 7 REMARK 465 ASN V 101 REMARK 465 SER V 102 REMARK 465 LEU V 103 REMARK 465 VAL V 104 REMARK 465 GLU V 105 REMARK 465 GLY V 106 REMARK 465 MET V 107 REMARK 465 ARG V 108 REMARK 465 MET V 109 REMARK 465 SER V 110 REMARK 465 ASN V 111 REMARK 465 LEU V 112 REMARK 465 VAL V 113 REMARK 465 THR V 114 REMARK 465 SER V 115 REMARK 465 VAL V 116 REMARK 465 VAL V 117 REMARK 465 LYS V 118 REMARK 465 HIS V 119 REMARK 465 ASP V 120 REMARK 465 GLU V 121 REMARK 465 GLU V 122 REMARK 465 ARG V 123 REMARK 465 ARG V 124 REMARK 465 VAL V 125 REMARK 465 ASN V 126 REMARK 465 PRO V 127 REMARK 465 ASP V 128 REMARK 465 ASP V 129 REMARK 465 SER V 130 REMARK 465 LYS V 131 REMARK 465 GLU V 132 REMARK 465 ASP V 133 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 V 45 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 1 ARG V 80 NE - CZ - NH2 ANGL. DEV. = 4.3 DEGREES REMARK 500 1 ARG V 90 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 2 ARG V 10 NE - CZ - NH1 ANGL. DEV. = -3.6 DEGREES REMARK 500 2 ARG V 10 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 2 ARG V 80 NE - CZ - NH2 ANGL. DEV. = 4.3 DEGREES REMARK 500 3 ARG V 25 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 ARG V 31 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 ARG V 80 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 ARG V 88 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 3 ARG V 90 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 4 ARG V 10 NE - CZ - NH2 ANGL. DEV. = 5.3 DEGREES REMARK 500 4 ARG V 45 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 4 ARG V 80 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 4 ARG V 90 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 5 ARG V 10 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 5 ARG V 25 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 5 ARG V 31 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 5 ARG V 80 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 6 ARG V 25 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 6 ARG V 45 NE - CZ - NH2 ANGL. DEV. = 4.3 DEGREES REMARK 500 6 ARG V 80 NE - CZ - NH2 ANGL. DEV. = 4.1 DEGREES REMARK 500 6 ARG V 88 NE - CZ - NH2 ANGL. DEV. = 4.5 DEGREES REMARK 500 7 ARG V 10 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 7 ARG V 25 NE - CZ - NH2 ANGL. DEV. = 3.9 DEGREES REMARK 500 7 ARG V 31 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 7 ARG V 90 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 8 ARG V 10 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 8 ARG V 45 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 8 ARG V 80 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 9 ARG V 10 NE - CZ - NH2 ANGL. DEV. = 5.1 DEGREES REMARK 500 9 ARG V 25 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 9 ARG V 80 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 9 ARG V 90 NE - CZ - NH2 ANGL. DEV. = 3.6 DEGREES REMARK 500 10 ARG V 25 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 10 ARG V 80 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG V 88 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 11 ARG V 10 NE - CZ - NH2 ANGL. DEV. = 3.7 DEGREES REMARK 500 11 ARG V 25 NE - CZ - NH2 ANGL. DEV. = 3.2 DEGREES REMARK 500 11 ARG V 45 NE - CZ - NH2 ANGL. DEV. = 4.1 DEGREES REMARK 500 11 ARG V 80 NE - CZ - NH2 ANGL. DEV. = 4.1 DEGREES REMARK 500 12 ARG V 45 NE - CZ - NH2 ANGL. DEV. = 3.4 DEGREES REMARK 500 12 ARG V 88 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 12 ARG V 90 NE - CZ - NH2 ANGL. DEV. = 3.1 DEGREES REMARK 500 13 ARG V 80 NE - CZ - NH2 ANGL. DEV. = 4.0 DEGREES REMARK 500 13 ARG V 88 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 13 ARG V 90 NE - CZ - NH2 ANGL. DEV. = 4.6 DEGREES REMARK 500 14 ARG V 31 NE - CZ - NH2 ANGL. DEV. = 3.0 DEGREES REMARK 500 14 ARG V 80 NE - CZ - NH2 ANGL. DEV. = 4.2 DEGREES REMARK 500 14 ARG V 88 NE - CZ - NH2 ANGL. DEV. = 3.5 DEGREES REMARK 500 REMARK 500 THIS ENTRY HAS 73 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 MET V 35 40.09 -149.27 REMARK 500 1 LEU V 47 19.55 55.56 REMARK 500 2 MET V 35 46.93 -154.02 REMARK 500 2 LEU V 47 19.92 57.34 REMARK 500 3 ASP V 59 -9.99 -56.24 REMARK 500 4 MET V 35 44.93 -143.65 REMARK 500 5 MET V 35 43.87 -154.03 REMARK 500 6 MET V 35 36.35 -154.58 REMARK 500 7 MET V 35 77.47 -152.98 REMARK 500 7 LEU V 47 19.33 58.79 REMARK 500 7 ASP V 59 -9.64 -57.38 REMARK 500 9 MET V 35 31.48 -149.79 REMARK 500 9 ASP V 59 -9.63 -58.87 REMARK 500 10 MET V 35 54.86 -147.31 REMARK 500 11 MET V 35 48.60 -157.12 REMARK 500 13 MET V 35 49.54 -158.72 REMARK 500 15 MET V 35 49.57 -141.81 REMARK 500 16 MET V 35 43.21 -146.58 REMARK 500 16 LEU V 47 19.20 55.32 REMARK 500 17 MET V 35 39.89 -153.75 REMARK 500 17 ASP V 59 -9.65 -55.75 REMARK 500 18 MET V 35 37.48 -151.82 REMARK 500 19 MET V 35 49.91 -153.51 REMARK 500 20 MET V 35 44.57 -155.29 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 7 ARG V 80 0.08 SIDE CHAIN REMARK 500 17 TYR V 49 0.07 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 34385 RELATED DB: BMRB REMARK 900 RIBOSOME BINDING FACTOR A (RBFA) REMARK 900 RELATED ID: 34561 RELATED DB: BMRB DBREF1 7AFQ V 1 133 UNP A0A5B7PAU8_ECOLX DBREF2 7AFQ V A0A5B7PAU8 1 133 SEQRES 1 V 133 MET ALA LYS GLU PHE GLY ARG PRO GLN ARG VAL ALA GLN SEQRES 2 V 133 GLU MET GLN LYS GLU ILE ALA LEU ILE LEU GLN ARG GLU SEQRES 3 V 133 ILE LYS ASP PRO ARG LEU GLY MET MET THR THR VAL SER SEQRES 4 V 133 GLY VAL GLU MET SER ARG ASP LEU ALA TYR ALA LYS VAL SEQRES 5 V 133 TYR VAL THR PHE LEU ASN ASP LYS ASP GLU ASP ALA VAL SEQRES 6 V 133 LYS ALA GLY ILE LYS ALA LEU GLN GLU ALA SER GLY PHE SEQRES 7 V 133 ILE ARG SER LEU LEU GLY LYS ALA MET ARG LEU ARG ILE SEQRES 8 V 133 VAL PRO GLU LEU THR PHE PHE TYR ASP ASN SER LEU VAL SEQRES 9 V 133 GLU GLY MET ARG MET SER ASN LEU VAL THR SER VAL VAL SEQRES 10 V 133 LYS HIS ASP GLU GLU ARG ARG VAL ASN PRO ASP ASP SER SEQRES 11 V 133 LYS GLU ASP HELIX 1 AA1 PRO V 8 GLU V 26 1 19 HELIX 2 AA2 LYS V 28 GLY V 33 5 6 HELIX 3 AA3 LEU V 57 LYS V 60 5 4 HELIX 4 AA4 ASP V 61 ALA V 75 1 15 HELIX 5 AA5 ALA V 75 ARG V 88 1 14 SHEET 1 AA1 3 THR V 37 MET V 43 0 SHEET 2 AA1 3 TYR V 49 THR V 55 -1 O THR V 55 N THR V 37 SHEET 3 AA1 3 GLU V 94 TYR V 99 1 O THR V 96 N VAL V 52 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