PDB Short entry for 2LMI HEADER RNA BINDING PROTEIN 01-DEC-11 2LMI TITLE NMR STRUCTURE OF THE PROTEIN BC040485 FROM HOMO SAPIENS COMPND MOL_ID: 1; COMPND 2 MOLECULE: G-RICH SEQUENCE FACTOR 1; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RRM 1 DOMAIN RESIDUES 140-245; COMPND 5 SYNONYM: GRSF-1; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: GRSF1; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_VECTOR: PSPEEDET KEYWDS G-RICH RNA SEQUENCE BINDING FACTOR, RNA BINDING DOMAIN, STRUCTURAL KEYWDS 2 GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PSI-BIOLOGY, KEYWDS 3 RNA BINDING PROTEIN, PARTNERSHIP FOR T-CELL BIOLOGY, TCELL EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR S.K.DUTTA,P.SERRANO,M.GERALT,K.WUTHRICH,JOINT CENTER FOR STRUCTURAL AUTHOR 2 GENOMICS (JCSG),PARTNERSHIP FOR T-CELL BIOLOGY (TCELL) REVDAT 3 14-JUN-23 2LMI 1 REMARK SEQADV REVDAT 2 21-OCT-15 2LMI 1 AUTHOR JRNL REVDAT 1 28-DEC-11 2LMI 0 JRNL AUTH S.K.DUTTA,P.SERRANO,M.GERALT,K.WUTHRICH, JRNL AUTH 2 JOINT CENTER FOR STRUCTURAL GENOMICS (JCSG), JRNL AUTH 3 PARTNERSHIP FOR T-CELL BIOLOGY (TCELL) JRNL TITL NMR STRUCTURE OF THE HUMAN RNA BINDING PROTEIN BC040485 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CYANA, OPAL REMARK 3 AUTHORS : G NTERT P. (CYANA), LUGINBUHL, GUNTERT, BILLETER REMARK 3 AND WUTHRICH (OPAL) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LMI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-DEC-11. REMARK 100 THE DEPOSITION ID IS D_1000102564. 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 : 0.080 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 1.2 MM [U-98% 13C; U-98% 15N] REMARK 210 PROTEIN, 20 MM SODIUM PHOSPHATE, REMARK 210 5 MM SODIUM AZIDE, 50 MM SODIUM REMARK 210 CHLORIDE, 95% H2O/5% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D CBCA(CO)NH; REMARK 210 3D HNCA; 3D HNCACB; 4D HACANH; REMARK 210 5D HACACONH; 5D CBCACONH; 3D 1H- REMARK 210 15N NOESY; 3D 1H-13C NOESY REMARK 210 ALIPHATIC; 3D 1H-13C NOESY REMARK 210 AROMATIC 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 : TOPSPIN, CARA REMARK 210 METHOD USED : MOLECULAR DYNAMICS REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 80 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: 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 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 36 CD - NE - CZ ANGL. DEV. = 8.5 DEGREES REMARK 500 4 TYR A 78 CB - CG - CD2 ANGL. DEV. = -3.8 DEGREES REMARK 500 5 ARG A 55 CD - NE - CZ ANGL. DEV. = 9.0 DEGREES REMARK 500 7 ARG A 55 NE - CZ - NH2 ANGL. DEV. = -3.5 DEGREES REMARK 500 8 ARG A 36 NE - CZ - NH2 ANGL. DEV. = -3.1 DEGREES REMARK 500 12 TYR A 78 CB - CG - CD2 ANGL. DEV. = -4.1 DEGREES REMARK 500 13 TYR A 78 CB - CG - CD2 ANGL. DEV. = -3.7 DEGREES REMARK 500 18 ARG A 54 NE - CZ - NH2 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 LYS A 3 92.05 -175.65 REMARK 500 1 GLU A 7 55.10 -142.28 REMARK 500 1 ASP A 10 26.35 -151.21 REMARK 500 1 ARG A 54 -59.32 -162.15 REMARK 500 1 ARG A 76 8.33 58.33 REMARK 500 1 GLU A 85 76.28 -164.59 REMARK 500 1 GLN A 102 21.01 -74.96 REMARK 500 1 SER A 106 164.20 64.28 REMARK 500 2 LYS A 3 94.63 -178.62 REMARK 500 2 GLU A 5 21.32 -147.44 REMARK 500 2 GLU A 7 15.28 -175.07 REMARK 500 2 ASP A 9 -169.05 -76.72 REMARK 500 2 PHE A 12 45.23 -92.99 REMARK 500 2 TRP A 21 -164.10 44.56 REMARK 500 2 PHE A 32 53.85 -93.65 REMARK 500 2 CYS A 35 -168.22 -122.20 REMARK 500 2 ARG A 50 -8.10 -55.12 REMARK 500 2 ARG A 54 -65.05 -148.47 REMARK 500 3 LYS A 3 52.74 -163.07 REMARK 500 3 CYS A 35 -164.82 -128.99 REMARK 500 3 GLN A 102 38.87 -74.75 REMARK 500 3 SER A 106 72.54 69.16 REMARK 500 4 LYS A 3 13.16 174.50 REMARK 500 4 GLU A 5 53.92 -105.87 REMARK 500 4 ASP A 10 70.73 -104.95 REMARK 500 4 GLN A 17 51.02 -163.23 REMARK 500 4 ASN A 39 -22.62 66.38 REMARK 500 4 GLU A 41 24.75 48.98 REMARK 500 4 LEU A 48 -179.51 -175.69 REMARK 500 4 ARG A 50 -18.36 -46.72 REMARK 500 4 ASP A 51 33.69 -144.42 REMARK 500 4 GLN A 81 33.58 -144.65 REMARK 500 4 GLN A 102 45.75 -86.62 REMARK 500 4 SER A 106 163.95 67.07 REMARK 500 5 SER A 22 77.98 -116.99 REMARK 500 5 PHE A 32 38.80 -90.13 REMARK 500 5 ASN A 39 -68.70 62.74 REMARK 500 5 PHE A 46 51.26 -146.34 REMARK 500 5 ARG A 54 -84.36 -99.65 REMARK 500 5 HIS A 75 18.88 -69.67 REMARK 500 5 GLN A 81 20.46 -145.11 REMARK 500 5 SER A 106 164.08 61.48 REMARK 500 6 LYS A 3 89.28 -173.02 REMARK 500 6 GLU A 7 41.94 -170.55 REMARK 500 6 ASP A 10 38.15 -78.53 REMARK 500 6 PRO A 20 -179.42 -67.04 REMARK 500 6 PHE A 32 51.02 -111.77 REMARK 500 6 CYS A 35 -164.33 -126.06 REMARK 500 6 ASN A 39 -2.98 64.36 REMARK 500 6 GLU A 41 -7.42 50.89 REMARK 500 REMARK 500 THIS ENTRY HAS 176 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 GLY A 80 GLN A 81 1 -145.12 REMARK 500 LEU A 101 GLN A 102 2 -144.73 REMARK 500 SER A 106 PRO A 107 11 148.22 REMARK 500 SER A 22 CYS A 23 14 148.15 REMARK 500 ASP A 93 VAL A 94 19 -145.43 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 1 ARG A 15 0.10 SIDE CHAIN REMARK 500 1 ARG A 38 0.08 SIDE CHAIN REMARK 500 1 ARG A 76 0.10 SIDE CHAIN REMARK 500 3 ARG A 15 0.10 SIDE CHAIN REMARK 500 3 ARG A 36 0.11 SIDE CHAIN REMARK 500 5 TYR A 83 0.09 SIDE CHAIN REMARK 500 6 ARG A 36 0.12 SIDE CHAIN REMARK 500 6 ARG A 38 0.08 SIDE CHAIN REMARK 500 7 ARG A 38 0.14 SIDE CHAIN REMARK 500 8 ARG A 54 0.08 SIDE CHAIN REMARK 500 8 ARG A 55 0.08 SIDE CHAIN REMARK 500 8 ARG A 76 0.10 SIDE CHAIN REMARK 500 9 ARG A 54 0.08 SIDE CHAIN REMARK 500 10 ARG A 36 0.11 SIDE CHAIN REMARK 500 14 ARG A 36 0.09 SIDE CHAIN REMARK 500 15 ARG A 38 0.08 SIDE CHAIN REMARK 500 15 ARG A 50 0.09 SIDE CHAIN REMARK 500 17 ARG A 38 0.10 SIDE CHAIN REMARK 500 18 ARG A 15 0.14 SIDE CHAIN REMARK 500 18 ARG A 38 0.12 SIDE CHAIN REMARK 500 19 ARG A 36 0.09 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 18118 RELATED DB: BMRB REMARK 900 RELATED ID: 421651 RELATED DB: TARGETDB DBREF 2LMI A 2 107 UNP Q12849 GRSF1_HUMAN 140 245 SEQADV 2LMI GLY A 1 UNP Q12849 EXPRESSION TAG SEQRES 1 A 107 GLY SER LYS LEU GLU GLU GLU VAL ASP ASP VAL PHE LEU SEQRES 2 A 107 ILE ARG ALA GLN GLY LEU PRO TRP SER CYS THR MET GLU SEQRES 3 A 107 ASP VAL LEU ASN PHE PHE SER ASP CYS ARG ILE ARG ASN SEQRES 4 A 107 GLY GLU ASN GLY ILE HIS PHE LEU LEU ASN ARG ASP GLY SEQRES 5 A 107 LYS ARG ARG GLY ASP ALA LEU ILE GLU MET GLU SER GLU SEQRES 6 A 107 GLN ASP VAL GLN LYS ALA LEU GLU LYS HIS ARG MET TYR SEQRES 7 A 107 MET GLY GLN ARG TYR VAL GLU VAL TYR GLU ILE ASN ASN SEQRES 8 A 107 GLU ASP VAL ASP ALA LEU MET LYS SER LEU GLN VAL LYS SEQRES 9 A 107 SER SER PRO HELIX 1 1 MET A 25 PHE A 32 1 8 HELIX 2 2 SER A 64 GLU A 73 1 10 HELIX 3 3 ASN A 90 SER A 100 1 11 SHEET 1 A 4 ILE A 44 HIS A 45 0 SHEET 2 A 4 ASP A 57 GLU A 61 -1 O LEU A 59 N HIS A 45 SHEET 3 A 4 LEU A 13 GLN A 17 -1 N ILE A 14 O ILE A 60 SHEET 4 A 4 TYR A 87 GLU A 88 -1 O TYR A 87 N ARG A 15 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