HEADER RNA BINDING PROTEIN 04-DEC-18 6Q3V TITLE CRYSTAL STRUCTURE OF HUMAN N4BP1 KH DOMAINS COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEDD4-BINDING PROTEIN 1; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: N4BP1; COMPND 5 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: N4BP1, KIAA0615; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS N4BP1 KH DOMAINS, RNA BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR A.GARG,U.HEINEMANN REVDAT 1 25-DEC-19 6Q3V 0 JRNL AUTH A.GARG,U.HEINEMANN JRNL TITL CRYSTAL STRUCTURE OF HUMAN N4BP1 KH DOMAINS JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.88 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.9_1692 REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE, REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER, REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY, REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON, REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI, REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : NULL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.88 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 35.58 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 3 NUMBER OF REFLECTIONS : 15566 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.183 REMARK 3 R VALUE (WORKING SET) : 0.181 REMARK 3 FREE R VALUE : 0.231 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 779 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS). REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE REMARK 3 1 35.5835 - 3.4195 1.00 2564 135 0.1533 0.1980 REMARK 3 2 3.4195 - 2.7145 1.00 2472 131 0.1892 0.2685 REMARK 3 3 2.7145 - 2.3714 1.00 2469 130 0.1963 0.2095 REMARK 3 4 2.3714 - 2.1546 1.00 2418 127 0.1967 0.2553 REMARK 3 5 2.1546 - 2.0002 1.00 2444 128 0.2115 0.2532 REMARK 3 6 2.0002 - 1.8823 0.99 2420 128 0.2805 0.3457 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : NULL REMARK 3 SOLVENT RADIUS : 1.11 REMARK 3 SHRINKAGE RADIUS : 0.90 REMARK 3 K_SOL : NULL REMARK 3 B_SOL : NULL REMARK 3 REMARK 3 ERROR ESTIMATES. REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.220 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 25.210 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 47.87 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : NULL REMARK 3 B22 (A**2) : NULL REMARK 3 B33 (A**2) : NULL REMARK 3 B12 (A**2) : NULL REMARK 3 B13 (A**2) : NULL REMARK 3 B23 (A**2) : NULL REMARK 3 REMARK 3 TWINNING INFORMATION. REMARK 3 FRACTION: NULL REMARK 3 OPERATOR: NULL REMARK 3 REMARK 3 DEVIATIONS FROM IDEAL VALUES. REMARK 3 RMSD COUNT REMARK 3 BOND : 0.006 1490 REMARK 3 ANGLE : 0.951 2021 REMARK 3 CHIRALITY : 0.038 232 REMARK 3 PLANARITY : 0.004 266 REMARK 3 DIHEDRAL : 13.376 561 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 3 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: CHAIN 'A' AND (RESID -1 THROUGH 68 ) REMARK 3 ORIGIN FOR THE GROUP (A): 47.0506 43.8346 21.3305 REMARK 3 T TENSOR REMARK 3 T11: 0.2166 T22: 0.2465 REMARK 3 T33: 0.2130 T12: -0.0006 REMARK 3 T13: -0.0808 T23: 0.0545 REMARK 3 L TENSOR REMARK 3 L11: 6.8873 L22: 7.1291 REMARK 3 L33: 6.1533 L12: 0.8863 REMARK 3 L13: -0.7629 L23: 0.7549 REMARK 3 S TENSOR REMARK 3 S11: -0.0436 S12: 0.5076 S13: 0.5164 REMARK 3 S21: -0.2219 S22: -0.0405 S23: -0.2090 REMARK 3 S31: -0.2651 S32: 0.2771 S33: 0.0785 REMARK 3 TLS GROUP : 2 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 69 THROUGH 135) REMARK 3 ORIGIN FOR THE GROUP (A): 30.9094 26.1306 22.9914 REMARK 3 T TENSOR REMARK 3 T11: 0.2900 T22: 0.2228 REMARK 3 T33: 0.3274 T12: -0.0066 REMARK 3 T13: 0.0429 T23: -0.0428 REMARK 3 L TENSOR REMARK 3 L11: 8.5315 L22: 1.2551 REMARK 3 L33: 1.5182 L12: -0.0962 REMARK 3 L13: 0.7854 L23: -0.2589 REMARK 3 S TENSOR REMARK 3 S11: 0.0586 S12: 0.1594 S13: -0.7694 REMARK 3 S21: 0.1500 S22: 0.0100 S23: 0.1358 REMARK 3 S31: 0.1376 S32: -0.1344 S33: -0.0504 REMARK 3 TLS GROUP : 3 REMARK 3 SELECTION: CHAIN 'A' AND (RESID 136 THROUGH 186 ) REMARK 3 ORIGIN FOR THE GROUP (A): 13.9983 30.4694 24.3617 REMARK 3 T TENSOR REMARK 3 T11: 0.2390 T22: 0.2768 REMARK 3 T33: 0.2982 T12: -0.0172 REMARK 3 T13: 0.0752 T23: -0.0340 REMARK 3 L TENSOR REMARK 3 L11: 2.3118 L22: 7.5614 REMARK 3 L33: 7.5597 L12: -1.8975 REMARK 3 L13: 0.3144 L23: 0.2742 REMARK 3 S TENSOR REMARK 3 S11: -0.0041 S12: -0.0571 S13: -0.0389 REMARK 3 S21: 0.5030 S22: -0.0058 S23: 0.5788 REMARK 3 S31: 0.2073 S32: -0.3875 S33: 0.0470 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 6Q3V COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 05-DEC-18. REMARK 100 THE DEPOSITION ID IS D_1200013258. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-DEC-16 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : BESSY REMARK 200 BEAMLINE : 14.1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.91841 REMARK 200 MONOCHROMATOR : SE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS PILATUS 6M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : XSCALE REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 15568 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.882 REMARK 200 RESOLUTION RANGE LOW (A) : 47.060 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.7 REMARK 200 DATA REDUNDANCY : 6.510 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.7800 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.88 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.95 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD REMARK 200 SOFTWARE USED: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.76 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.27 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: SODIUM MALONATE, VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 277K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 62 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+2/3 REMARK 290 3555 -X+Y,-X,Z+1/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+2/3 REMARK 290 6555 X-Y,X,Z+1/3 REMARK 290 REMARK 290 WHERE NNN -> OPERATOR NUMBER REMARK 290 MMM -> TRANSLATION VECTOR REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY TRANSFORMATIONS REMARK 290 THE FOLLOWING TRANSFORMATIONS OPERATE ON THE ATOM/HETATM REMARK 290 RECORDS IN THIS ENTRY TO PRODUCE CRYSTALLOGRAPHICALLY REMARK 290 RELATED MOLECULES. REMARK 290 SMTRY1 1 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 1 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 1 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 2 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 18.48467 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 9.24233 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 18.48467 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 9.24233 REMARK 290 REMARK 290 REMARK: NULL 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: 10570 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH A 305 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 LEU A 40 CG CD1 CD2 REMARK 470 LYS A 78 CG CD CE NZ REMARK 470 LYS A 137 CG CD CE NZ REMARK 470 GLU A 138 CG CD OE1 OE2 REMARK 470 ASN A 139 CG OD1 ND2 REMARK 470 LEU A 140 CG CD1 CD2 REMARK 470 LYS A 145 CG CD CE NZ REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS IN SAME ASYMMETRIC UNIT 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 O HOH A 234 O HOH A 283 2.15 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 ALA A 36 -43.98 60.66 REMARK 500 PRO A 141 140.17 -35.45 REMARK 500 ASP A 162 -159.25 -151.06 REMARK 500 REMARK 500 REMARK: NULL DBREF 6Q3V A 1 186 UNP O75113 N4BP1_HUMAN 8 193 SEQADV 6Q3V GLY A -1 UNP O75113 EXPRESSION TAG SEQADV 6Q3V SER A 0 UNP O75113 EXPRESSION TAG SEQRES 1 A 188 GLY SER ASP GLU PHE THR ALA PRO ALA GLU LYS ALA GLU SEQRES 2 A 188 LEU LEU GLU GLN SER ARG GLY ARG ILE GLU GLY LEU PHE SEQRES 3 A 188 GLY VAL SER LEU ALA VAL LEU GLY ALA LEU GLY ALA GLU SEQRES 4 A 188 GLU PRO LEU PRO ALA ARG ILE TRP LEU GLN LEU CYS GLY SEQRES 5 A 188 ALA GLN GLU ALA VAL HIS SER ALA LYS GLU TYR ILE LYS SEQRES 6 A 188 GLY ILE CYS GLU PRO GLU LEU GLU GLU ARG GLU CYS TYR SEQRES 7 A 188 PRO LYS ASP MET HIS CYS ILE PHE VAL GLY ALA GLU SER SEQRES 8 A 188 LEU PHE LEU LYS SER LEU ILE GLN ASP THR CYS ALA ASP SEQRES 9 A 188 LEU CYS ILE LEU ASP ILE GLY LEU LEU GLY ILE ARG GLY SEQRES 10 A 188 SER ALA GLU ALA VAL VAL MET ALA ARG SER HIS ILE GLN SEQRES 11 A 188 GLN PHE VAL LYS LEU PHE GLU ASN LYS GLU ASN LEU PRO SEQRES 12 A 188 SER SER GLN LYS GLU SER GLU VAL LYS ARG GLU PHE LYS SEQRES 13 A 188 GLN PHE VAL GLU ALA HIS ALA ASP ASN TYR THR MET ASP SEQRES 14 A 188 LEU LEU ILE LEU PRO THR SER LEU LYS LYS GLU LEU LEU SEQRES 15 A 188 THR LEU THR GLN GLY GLU FORMUL 2 HOH *106(H2 O) HELIX 1 AA1 LYS A 9 GLY A 25 1 17 HELIX 2 AA2 ALA A 51 GLU A 67 1 17 HELIX 3 AA3 PRO A 77 MET A 80 5 4 HELIX 4 AA4 HIS A 81 GLY A 86 1 6 HELIX 5 AA5 SER A 89 CYS A 100 1 12 HELIX 6 AA6 SER A 116 ASN A 136 1 21 HELIX 7 AA7 SER A 143 ALA A 159 1 17 HELIX 8 AA8 TYR A 164 ILE A 170 1 7 HELIX 9 AA9 PRO A 172 GLY A 185 1 14 SHEET 1 AA1 3 SER A 0 PRO A 6 0 SHEET 2 AA1 3 ARG A 43 CYS A 49 -1 O LEU A 46 N PHE A 3 SHEET 3 AA1 3 SER A 27 VAL A 30 -1 N ALA A 29 O GLN A 47 SHEET 1 AA2 3 LEU A 70 CYS A 75 0 SHEET 2 AA2 3 LEU A 110 GLY A 115 -1 O ILE A 113 N GLU A 72 SHEET 3 AA2 3 ASP A 102 ASP A 107 -1 N ASP A 102 O ARG A 114 CRYST1 108.690 108.690 27.727 90.00 90.00 120.00 P 62 6 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 0.009200 0.005312 0.000000 0.00000 SCALE2 0.000000 0.010624 0.000000 0.00000 SCALE3 0.000000 0.000000 0.036066 0.00000