HEADER DNA BINDING PROTEIN, CHAPERONE 09-NOV-11 2LLH TITLE NMR STRUCTURE OF NPM1_C70 COMPND MOL_ID: 1; COMPND 2 MOLECULE: NUCLEOPHOSMIN; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: NUCLEOLAR LOCALIZATION REGION RESIDUES 225-294; COMPND 5 SYNONYM: NPM, NUCLEOLAR PHOSPHOPROTEIN B23, NUCLEOLAR PROTEIN NO38, COMPND 6 NUMATRIN; COMPND 7 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: NPM1, NPM; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR: PET28+(A) KEYWDS NUCLEOLAR, CHAPERONE, ONCOPROTEIN, DNA BINDING PROTEIN EXPDTA SOLUTION NMR NUMMDL 20 AUTHOR L.BANCI,I.BERTINI,M.BRUNORI,A.DI MATTEO,L.FEDERICI,A.GALLO,C.LO AUTHOR 2 STERZO,M.MORI REVDAT 4 15-MAY-24 2LLH 1 REMARK REVDAT 3 14-JUN-23 2LLH 1 REMARK SEQADV REVDAT 2 22-AUG-12 2LLH 1 JRNL REVDAT 1 27-JUN-12 2LLH 0 JRNL AUTH A.GALLO,C.LO STERZO,M.MORI,A.DI MATTEO,I.BERTINI,L.BANCI, JRNL AUTH 2 M.BRUNORI,L.FEDERICI JRNL TITL STRUCTURE OF NUCLEOPHOSMIN DNA-BINDING DOMAIN AND ANALYSIS JRNL TITL 2 OF ITS COMPLEX WITH A G-QUADRUPLEX SEQUENCE FROM THE C-MYC JRNL TITL 3 PROMOTER. JRNL REF J.BIOL.CHEM. V. 287 26539 2012 JRNL REFN ISSN 0021-9258 JRNL PMID 22707729 JRNL DOI 10.1074/JBC.M112.371013 REMARK 2 REMARK 2 RESOLUTION. NOT APPLICABLE. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : TOPSPIN 2.1, AMBER 11.0 REMARK 3 AUTHORS : BRUKER BIOSPIN (TOPSPIN), CASE, DARDEN, CHEATHAM, REMARK 3 III, SIMMERLING, WANG, DUKE, LUO, AND KOLLM (AMBER) REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2LLH COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 17-NOV-11. REMARK 100 THE DEPOSITION ID IS D_1000102527. REMARK 210 REMARK 210 EXPERIMENTAL DETAILS REMARK 210 EXPERIMENT TYPE : NMR REMARK 210 TEMPERATURE (KELVIN) : 298 REMARK 210 PH : 7.2 REMARK 210 IONIC STRENGTH : 20 REMARK 210 PRESSURE : AMBIENT REMARK 210 SAMPLE CONTENTS : 0.5 MM [U-15N] PROTEIN, 20 MM REMARK 210 SODIUM PHOSPHATE, 90% H2O/10% REMARK 210 D2O; 0.5 MM [U-13C; U-15N] REMARK 210 PROTEIN, 20 MM SODIUM PHOSPHATE, REMARK 210 90% H2O/10% D2O REMARK 210 REMARK 210 NMR EXPERIMENTS CONDUCTED : 2D 1H-15N HSQC; 3D CBCA(CO)NH; REMARK 210 3D HNCO; 3D HNCA; 3D HNCACB; 3D REMARK 210 HBHA(CO)NH; 3D HN(CO)CA; 3D REMARK 210 HN(CA)CO; 3D HCCH-TOCSY; 2D 1H- REMARK 210 1H NOESY; 3D 1H-13C NOESY; 3D 1H- REMARK 210 15N NOESY REMARK 210 SPECTROMETER FIELD STRENGTH : 900 MHZ; 700 MHZ; 500 MHZ REMARK 210 SPECTROMETER MODEL : AVANCE REMARK 210 SPECTROMETER MANUFACTURER : BRUKER REMARK 210 REMARK 210 STRUCTURE DETERMINATION. REMARK 210 SOFTWARE USED : TOPSPIN 2.1, CARA 2.1, TALOS, REMARK 210 CYANA 2.1, PSVS REMARK 210 METHOD USED : MOLECULAR DYNAMICS, SIMULATED REMARK 210 ANNEALING REMARK 210 REMARK 210 CONFORMERS, NUMBER CALCULATED : 400 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 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 GLY A -3 REMARK 465 SER A -2 REMARK 465 HIS A -1 REMARK 465 MET A 0 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 67 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 2 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 3 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 4 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 3.7 DEGREES REMARK 500 4 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 5 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 4.0 DEGREES REMARK 500 6 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 7 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 7 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 9 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 3.9 DEGREES REMARK 500 9 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 10 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 12 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 3.4 DEGREES REMARK 500 12 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 13 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 3.0 DEGREES REMARK 500 14 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.8 DEGREES REMARK 500 15 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.3 DEGREES REMARK 500 17 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 3.2 DEGREES REMARK 500 17 ARG A 67 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 19 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 20 ARG A 53 NE - CZ - NH1 ANGL. DEV. = 4.1 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 PHE A 4 -39.07 -145.47 REMARK 500 1 GLN A 7 -63.39 -146.44 REMARK 500 1 LYS A 9 -164.69 46.96 REMARK 500 1 LYS A 12 -45.88 -157.33 REMARK 500 1 THR A 13 76.22 46.27 REMARK 500 1 PRO A 17 -167.17 -65.36 REMARK 500 1 GLU A 32 -60.35 -96.33 REMARK 500 1 SER A 69 45.42 -83.15 REMARK 500 2 GLN A 7 -68.21 -136.85 REMARK 500 2 LYS A 9 -31.19 -142.30 REMARK 500 2 VAL A 20 -25.24 58.87 REMARK 500 3 PHE A 4 -171.07 55.80 REMARK 500 3 LYS A 6 48.36 -163.58 REMARK 500 3 LYS A 12 40.12 -142.04 REMARK 500 3 PRO A 17 -176.90 -55.51 REMARK 500 3 SER A 19 -164.37 -111.54 REMARK 500 3 PHE A 52 -90.35 -135.06 REMARK 500 3 ARG A 53 -53.62 -162.79 REMARK 500 3 MET A 54 109.44 45.83 REMARK 500 4 LYS A 9 80.65 50.71 REMARK 500 4 PRO A 17 173.54 -52.48 REMARK 500 4 LEU A 37 151.41 67.89 REMARK 500 5 SER A 36 69.58 -108.71 REMARK 500 5 ASP A 56 89.29 -67.78 REMARK 500 6 SER A 3 128.80 61.44 REMARK 500 6 LYS A 5 -161.29 61.67 REMARK 500 6 LYS A 6 132.35 69.56 REMARK 500 6 GLN A 7 -69.41 62.19 REMARK 500 6 GLU A 8 -25.38 59.08 REMARK 500 6 LYS A 12 176.01 56.67 REMARK 500 6 SER A 18 17.54 -68.32 REMARK 500 6 SER A 19 -81.85 -135.21 REMARK 500 6 PHE A 52 136.89 -171.35 REMARK 500 6 THR A 55 -21.53 52.67 REMARK 500 7 SER A 36 -6.29 -161.46 REMARK 500 7 THR A 55 -29.49 56.55 REMARK 500 7 SER A 69 43.57 -85.99 REMARK 500 8 LYS A 5 171.53 56.33 REMARK 500 8 GLN A 7 -37.51 -135.76 REMARK 500 8 GLU A 8 144.73 62.12 REMARK 500 8 PRO A 17 160.93 -48.77 REMARK 500 8 MET A 54 73.35 41.59 REMARK 500 9 SER A 3 159.56 58.01 REMARK 500 9 PHE A 4 -36.47 -135.54 REMARK 500 9 GLN A 7 -61.82 -138.24 REMARK 500 9 GLU A 8 -43.08 59.31 REMARK 500 9 SER A 18 32.59 -80.57 REMARK 500 9 PHE A 52 -27.59 -152.97 REMARK 500 9 ARG A 53 93.86 53.30 REMARK 500 9 THR A 55 -36.20 64.31 REMARK 500 REMARK 500 THIS ENTRY HAS 112 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2VXD RELATED DB: PDB REMARK 900 RELATED ID: 18048 RELATED DB: BMRB DBREF 2LLH A 1 70 UNP P06748 NPM_HUMAN 225 294 SEQADV 2LLH GLY A -3 UNP P06748 EXPRESSION TAG SEQADV 2LLH SER A -2 UNP P06748 EXPRESSION TAG SEQADV 2LLH HIS A -1 UNP P06748 EXPRESSION TAG SEQADV 2LLH MET A 0 UNP P06748 EXPRESSION TAG SEQRES 1 A 74 GLY SER HIS MET GLN GLU SER PHE LYS LYS GLN GLU LYS SEQRES 2 A 74 THR PRO LYS THR PRO LYS GLY PRO SER SER VAL GLU ASP SEQRES 3 A 74 ILE LYS ALA LYS MET GLN ALA SER ILE GLU LYS GLY GLY SEQRES 4 A 74 SER LEU PRO LYS VAL GLU ALA LYS PHE ILE ASN TYR VAL SEQRES 5 A 74 LYS ASN CYS PHE ARG MET THR ASP GLN GLU ALA ILE GLN SEQRES 6 A 74 ASP LEU TRP GLN TRP ARG LYS SER LEU HELIX 1 1 SER A 19 GLY A 34 1 16 HELIX 2 2 VAL A 40 PHE A 52 1 13 HELIX 3 3 ASP A 56 SER A 69 1 14 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