PDB Short entry for 2P39 HEADER SIGNALING PROTEIN 08-MAR-07 2P39 TITLE CRYSTAL STRUCTURE OF HUMAN FGF23 COMPND MOL_ID: 1; COMPND 2 MOLECULE: FIBROBLAST GROWTH FACTOR 23; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: FGF-23, TUMOR-DERIVED HYPOPHOSPHATEMIA-INDUCING FACTOR; 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: FGF23, HYPF; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21 (DE3) PLYS-S KEYWDS ATYPICAL BETA-TREFOIL FOLD, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR M.MOHAMMADI REVDAT 5 30-AUG-23 2P39 1 HETSYN REVDAT 4 29-JUL-20 2P39 1 COMPND REMARK HET HETNAM REVDAT 4 2 1 FORMUL LINK SITE ATOM REVDAT 3 24-FEB-09 2P39 1 VERSN REVDAT 2 24-APR-07 2P39 1 JRNL REVDAT 1 10-APR-07 2P39 0 JRNL AUTH R.GOETZ,A.BEENKEN,O.A.IBRAHIMI,J.KALININA,S.K.OLSEN, JRNL AUTH 2 A.V.ELISEENKOVA,C.XU,T.A.NEUBERT,F.ZHANG,R.J.LINHARDT,X.YU, JRNL AUTH 3 K.E.WHITE,T.INAGAKI,S.A.KLIEWER,M.YAMAMOTO,H.KUROSU,Y.OGAWA, JRNL AUTH 4 M.KURO-O,B.LANSKE,M.S.RAZZAQUE,M.MOHAMMADI JRNL TITL MOLECULAR INSIGHTS INTO THE KLOTHO-DEPENDENT, ENDOCRINE MODE JRNL TITL 2 OF ACTION OF FIBROBLAST GROWTH FACTOR 19 SUBFAMILY MEMBERS. JRNL REF MOL.CELL.BIOL. V. 27 3417 2007 JRNL REFN ISSN 0270-7306 JRNL PMID 17339340 JRNL DOI 10.1128/MCB.02249-06 REMARK 2 REMARK 2 RESOLUTION. 1.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.1 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 25.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 25152 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : THROUGHOUT REMARK 3 FREE R VALUE TEST SET SELECTION : RANDOM REMARK 3 R VALUE (WORKING SET) : 0.203 REMARK 3 FREE R VALUE : 0.214 REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : 2496 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1113 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 55 REMARK 3 SOLVENT ATOMS : 93 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -2.24300 REMARK 3 B22 (A**2) : 2.01600 REMARK 3 B33 (A**2) : 0.22700 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.006 REMARK 3 BOND ANGLES (DEGREES) : NULL REMARK 3 DIHEDRAL ANGLES (DEGREES) : NULL REMARK 3 IMPROPER ANGLES (DEGREES) : 0.726 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : NULL REMARK 3 KSOL : NULL REMARK 3 BSOL : NULL REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 2P39 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 13-MAR-07. REMARK 100 THE DEPOSITION ID IS D_1000041910. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 29-JUL-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : NSLS REMARK 200 BEAMLINE : X4A REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97924 REMARK 200 MONOCHROMATOR : KOHZU DOUBLE CRYSTAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25550 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5 REMARK 200 DATA REDUNDANCY : 11.90 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.05900 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 26.1000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.55 REMARK 200 COMPLETENESS FOR SHELL (%) : 95.6 REMARK 200 DATA REDUNDANCY IN SHELL : 5.70 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.29700 REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 2P23 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 43.37 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM TRIS-HCL, 1.0 M (NH4)2SO4, 10 REMARK 280 MM [CO(NH3)6]CL3, PH 8.5, VAPOR DIFFUSION, HANGING DROP, REMARK 280 TEMPERATURE 298K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 REMARK 290 4555 X+1/2,-Y+1/2,-Z 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 19.40550 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 42.46550 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 23.54700 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 42.46550 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.40550 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 23.54700 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 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 APPLY THE FOLLOWING TO CHAINS: A, B 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 TYR A 25 REMARK 465 PRO A 26 REMARK 465 ASN A 27 REMARK 465 ALA A 28 REMARK 465 THR A 171 REMARK 465 PRO A 172 REMARK 465 ILE A 173 REMARK 465 PRO A 174 REMARK 465 ARG A 175 REMARK 465 ARG A 176 REMARK 465 HIS A 177 REMARK 465 THR A 178 REMARK 465 ARG A 179 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 LYS A 57 CG CD CE NZ REMARK 470 ARG A 76 CG CD NE CZ NH1 NH2 REMARK 470 ARG A 99 CG CD NE CZ NH1 NH2 REMARK 470 GLU A 111 CG CD OE1 OE2 REMARK 470 GLU A 121 CG CD OE1 OE2 REMARK 470 GLN A 131 CG CD OE1 NE2 REMARK 470 ARG A 161 CG CD NE CZ NH1 NH2 REMARK 470 ASN A 170 CG OD1 ND2 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 SER A 35 14.90 -142.03 REMARK 500 ASP A 62 -157.29 -147.48 REMARK 500 GLU A 78 -164.42 -117.88 REMARK 500 HIS A 133 -17.73 72.62 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2P23 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF HUMAN FGF19 DBREF 2P39 A 25 179 UNP Q9GZV9 FGF23_HUMAN 25 179 SEQRES 1 A 155 TYR PRO ASN ALA SER PRO LEU LEU GLY SER SER TRP GLY SEQRES 2 A 155 GLY LEU ILE HIS LEU TYR THR ALA THR ALA ARG ASN SER SEQRES 3 A 155 TYR HIS LEU GLN ILE HIS LYS ASN GLY HIS VAL ASP GLY SEQRES 4 A 155 ALA PRO HIS GLN THR ILE TYR SER ALA LEU MET ILE ARG SEQRES 5 A 155 SER GLU ASP ALA GLY PHE VAL VAL ILE THR GLY VAL MET SEQRES 6 A 155 SER ARG ARG TYR LEU CYS MET ASP PHE ARG GLY ASN ILE SEQRES 7 A 155 PHE GLY SER HIS TYR PHE ASP PRO GLU ASN CYS ARG PHE SEQRES 8 A 155 GLN HIS GLN THR LEU GLU ASN GLY TYR ASP VAL TYR HIS SEQRES 9 A 155 SER PRO GLN TYR HIS PHE LEU VAL SER LEU GLY ARG ALA SEQRES 10 A 155 LYS ARG ALA PHE LEU PRO GLY MET ASN PRO PRO PRO TYR SEQRES 11 A 155 SER GLN PHE LEU SER ARG ARG ASN GLU ILE PRO LEU ILE SEQRES 12 A 155 HIS PHE ASN THR PRO ILE PRO ARG ARG HIS THR ARG HET GU4 B 1 27 HET YYJ B 2 28 HETNAM GU4 2,3,4,6-TETRA-O-SULFONATO-ALPHA-D-GLUCOPYRANOSE HETNAM YYJ 1,3,4,6-TETRA-O-SULFO-BETA-D-FRUCTOFURANOSE HETSYN GU4 2,3,4,6-TETRA-O-SULFONATO-ALPHA-D-GLUCOSE; 2,3,4,6- HETSYN 2 GU4 TETRA-O-SULFONATO-D-GLUCOSE; 2,3,4,6-TETRA-O- HETSYN 3 GU4 SULFONATO-GLUCOSE FORMUL 2 GU4 C6 H12 O18 S4 FORMUL 2 YYJ C6 H12 O18 S4 FORMUL 3 HOH *93(H2 O) HELIX 1 1 PRO A 152 GLN A 156 5 5 HELIX 2 2 PRO A 165 PHE A 169 5 5 SHEET 1 A 2 ILE A 40 TYR A 43 0 SHEET 2 A 2 LEU A 158 ARG A 161 -1 O ARG A 160 N HIS A 41 SHEET 1 B 2 HIS A 52 ILE A 55 0 SHEET 2 B 2 VAL A 61 ALA A 64 -1 O ASP A 62 N GLN A 54 SHEET 1 C 4 LEU A 73 SER A 77 0 SHEET 2 C 4 PHE A 82 GLY A 87 -1 O VAL A 84 N ARG A 76 SHEET 3 C 4 ARG A 92 MET A 96 -1 O ARG A 92 N GLY A 87 SHEET 4 C 4 ILE A 102 SER A 105 -1 O SER A 105 N TYR A 93 SHEET 1 D 4 LEU A 73 SER A 77 0 SHEET 2 D 4 PHE A 82 GLY A 87 -1 O VAL A 84 N ARG A 76 SHEET 3 D 4 PHE A 115 THR A 119 -1 O PHE A 115 N VAL A 83 SHEET 4 D 4 ASP A 125 HIS A 128 -1 O HIS A 128 N GLN A 116 SSBOND 1 CYS A 95 CYS A 113 1555 1555 2.34 LINK C1 GU4 B 1 O2 YYJ B 2 1555 1555 1.45 CRYST1 38.811 47.094 84.931 90.00 90.00 90.00 P 21 21 21 4 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 0.025766 0.000000 0.000000 0.00000 SCALE2 0.000000 0.021234 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011774 0.00000