HEADER PROTEIN BINDING 18-JUN-13 4L9H TITLE CRYSTAL STRUCTURE OF THE FP DOMAIN OF HUMAN F-BOX PROTEIN FBXO7(SEMET) COMPND MOL_ID: 1; COMPND 2 MOLECULE: F-BOX ONLY PROTEIN 7; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: UNP RESIDUES 180-335; 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: FBX7, FBXO7, HUMAN FBXO7; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID KEYWDS ALPHA/BETA FOLD, PROTEIN BINDING EXPDTA X-RAY DIFFRACTION AUTHOR Z.DU,X.HUANG,J.SHANG,Y.YANG,G.WANG REVDAT 3 08-OCT-14 4L9H 1 AUTHOR REVDAT 2 24-SEP-14 4L9H 1 JRNL REVDAT 1 15-JAN-14 4L9H 0 JRNL AUTH J.SHANG,G.WANG,Y.YANG,X.HUANG,Z.DU JRNL TITL STRUCTURE OF THE FP DOMAIN OF FBXO7 REVEALS A NOVEL MODE OF JRNL TITL 2 PROTEIN-PROTEIN INTERACTION. JRNL REF ACTA CRYSTALLOGR.,SECT.D V. 70 155 2014 JRNL REFN ISSN 0907-4449 JRNL PMID 24419388 JRNL DOI 10.1107/S1399004713025820 REMARK 2 REMARK 2 RESOLUTION. 2.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (PHENIX.REFINE: 1.8.2_1309) REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE- REMARK 3 : KUNSTLEVE,LI-WEI HUNG,ROBERT IMMORMINO, REMARK 3 : TOM IOERGER,AIRLIE MCCOY,ERIK MCKEE,NIGEL REMARK 3 : MORIARTY,REETAL PAI,RANDY READ,JANE REMARK 3 : RICHARDSON,DAVID RICHARDSON,TOD ROMO,JIM REMARK 3 : SACCHETTINI,NICHOLAS SAUTER,JACOB SMITH, REMARK 3 : LAURENT STORONI,TOM TERWILLIGER,PETER REMARK 3 : ZWART REMARK 3 REMARK 3 REFINEMENT TARGET : MLHL REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.77 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.530 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 10718 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.205 REMARK 3 R VALUE (WORKING SET) : 0.201 REMARK 3 FREE R VALUE : 0.234 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1072 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 40.7732 - 3.9992 1.00 1320 147 0.1836 0.2301 REMARK 3 2 3.9992 - 3.1747 1.00 1222 136 0.1870 0.2019 REMARK 3 3 3.1747 - 2.7735 1.00 1210 135 0.2228 0.2155 REMARK 3 4 2.7735 - 2.5199 1.00 1182 131 0.2010 0.2143 REMARK 3 5 2.5199 - 2.3394 1.00 1188 132 0.2159 0.2570 REMARK 3 6 2.3394 - 2.2014 1.00 1177 130 0.2169 0.3015 REMARK 3 7 2.2014 - 2.0912 1.00 1168 130 0.2191 0.2559 REMARK 3 8 2.0912 - 2.0002 1.00 1179 131 0.2412 0.3301 REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL 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) : 0.180 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 22.820 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 28.43 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 : 0.004 1234 REMARK 3 ANGLE : 0.879 1674 REMARK 3 CHIRALITY : 0.056 198 REMARK 3 PLANARITY : 0.007 211 REMARK 3 DIHEDRAL : 14.066 466 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL 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 4L9H COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-JUN-13. REMARK 100 THE RCSB ID CODE IS RCSB080349. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 21-ID-D REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97872 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10718 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.000 REMARK 200 RESOLUTION RANGE LOW (A) : 99.991 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : NULL REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL 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: NULL REMARK 200 SOFTWARE USED: NULL REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 40.66 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 3350, MOPS 7.0, KBR, PH 8.0, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4 REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4 REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4 REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4 REMARK 290 7555 Y,X,-Z REMARK 290 8555 -Y,-X,-Z+1/2 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 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 44.66000 REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 28.82500 REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 28.82500 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 66.99000 REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 28.82500 REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 28.82500 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 22.33000 REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 28.82500 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 28.82500 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 66.99000 REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 28.82500 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 28.82500 REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 22.33000 REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 44.66000 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 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. (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 465 IDENTIFIER; SSSEQ=SEQUENCE NUMBER; I=INSERTION CODE.) REMARK 465 REMARK 465 M RES C SSSEQI REMARK 465 GLY A 331 REMARK 465 LEU A 332 REMARK 465 VAL A 333 REMARK 465 VAL A 334 REMARK 465 LEU A 335 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 448 O HOH A 450 2.16 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 ASN A 269 22.82 47.51 REMARK 500 GLU A 292 -143.41 -119.68 REMARK 500 LEU A 312 -59.83 -133.77 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 4L9C RELATED DB: PDB DBREF 4L9H A 180 335 UNP Q9Y3I1 FBX7_HUMAN 180 335 SEQADV 4L9H GLY A 176 UNP Q9Y3I1 EXPRESSION TAG SEQADV 4L9H PRO A 177 UNP Q9Y3I1 EXPRESSION TAG SEQADV 4L9H SER A 178 UNP Q9Y3I1 EXPRESSION TAG SEQADV 4L9H SER A 179 UNP Q9Y3I1 EXPRESSION TAG SEQRES 1 A 160 GLY PRO SER SER PRO HIS SER LEU GLU THR LEU TYR GLN SEQRES 2 A 160 SER ALA ASP CYS SER ASP ALA ASN ASP ALA LEU ILE VAL SEQRES 3 A 160 LEU ILE HIS LEU LEU MSE LEU GLU SER GLY TYR ILE PRO SEQRES 4 A 160 GLN GLY THR GLU ALA LYS ALA LEU SER MSE PRO GLU LYS SEQRES 5 A 160 TRP LYS LEU SER GLY VAL TYR LYS LEU GLN TYR MSE HIS SEQRES 6 A 160 PRO LEU CYS GLU GLY SER SER ALA THR LEU THR CYS VAL SEQRES 7 A 160 PRO LEU GLY ASN LEU ILE VAL VAL ASN ALA THR LEU LYS SEQRES 8 A 160 ILE ASN ASN GLU ILE ARG SER VAL LYS ARG LEU GLN LEU SEQRES 9 A 160 LEU PRO GLU SER PHE ILE CYS LYS GLU LYS LEU GLY GLU SEQRES 10 A 160 ASN VAL ALA ASN ILE TYR LYS ASP LEU GLN LYS LEU SER SEQRES 11 A 160 ARG LEU PHE LYS ASP GLN LEU VAL TYR PRO LEU LEU ALA SEQRES 12 A 160 PHE THR ARG GLN ALA LEU ASN LEU PRO ASP VAL PHE GLY SEQRES 13 A 160 LEU VAL VAL LEU MODRES 4L9H MSE A 207 MET SELENOMETHIONINE MODRES 4L9H MSE A 224 MET SELENOMETHIONINE MODRES 4L9H MSE A 239 MET SELENOMETHIONINE HET MSE A 207 8 HET MSE A 224 8 HET MSE A 239 8 HETNAM MSE SELENOMETHIONINE FORMUL 1 MSE 3(C5 H11 N O2 SE) FORMUL 2 HOH *56(H2 O) HELIX 1 1 PRO A 180 ASP A 191 1 12 HELIX 2 2 ASP A 194 SER A 210 1 17 HELIX 3 3 LEU A 280 PHE A 284 5 5 HELIX 4 4 CYS A 286 LEU A 290 5 5 HELIX 5 5 ASN A 293 TYR A 298 1 6 HELIX 6 6 ASP A 300 LEU A 312 1 13 HELIX 7 7 LEU A 312 LEU A 324 1 13 SHEET 1 A 3 ILE A 213 PRO A 214 0 SHEET 2 A 3 VAL A 233 MSE A 239 -1 O MSE A 239 N ILE A 213 SHEET 3 A 3 LYS A 229 LEU A 230 -1 N LEU A 230 O VAL A 233 SHEET 1 B 5 ILE A 213 PRO A 214 0 SHEET 2 B 5 VAL A 233 MSE A 239 -1 O MSE A 239 N ILE A 213 SHEET 3 B 5 SER A 247 LEU A 255 -1 O ALA A 248 N TYR A 238 SHEET 4 B 5 LEU A 258 ILE A 267 -1 O VAL A 260 N VAL A 253 SHEET 5 B 5 GLU A 270 LEU A 279 -1 O ARG A 272 N LEU A 265 LINK C LEU A 206 N MSE A 207 1555 1555 1.33 LINK C MSE A 207 N LEU A 208 1555 1555 1.33 LINK C SER A 223 N MSE A 224 1555 1555 1.33 LINK C MSE A 224 N PRO A 225 1555 1555 1.34 LINK C TYR A 238 N MSE A 239 1555 1555 1.33 LINK C MSE A 239 N HIS A 240 1555 1555 1.33 CRYST1 57.650 57.650 89.320 90.00 90.00 90.00 P 43 21 2 8 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 0.017346 0.000000 0.000000 0.00000 SCALE2 0.000000 0.017346 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011196 0.00000 MASTER 258 0 3 7 8 0 0 6 0 0 0 13 END