PDB Short entry for 5MR9 HEADER SIGNALING PROTEIN 21-DEC-16 5MR9 TITLE LIGAND-RECEPTOR COMPLEX. COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEURTURIN; COMPND 3 CHAIN: A, B; COMPND 4 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: NRTN; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS COMPLEX, SIGNALLING, RECEPTOR, SIGNALING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.SANDMARK,L.OSTER,A.AAGAARD,R.G.ROTH,G.DAHL REVDAT 2 16-OCT-19 5MR9 1 REMARK REVDAT 1 17-JAN-18 5MR9 0 JRNL AUTH J.SANDMARK,G.DAHL,L.OSTER,B.XU,P.JOHANSSON,T.AKERUD, JRNL AUTH 2 A.AAGAARD,P.DAVIDSSON,M.SORHEDE-WINZELL,G.J.RAINEY,R.G.ROTH JRNL TITL STRUCTURE AND BIOPHYSICAL CHARACTERISATION OF THE HUMAN JRNL TITL 2 COMPLEX - A ROLE FOR HEPARAN SULFATE JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 2.40 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : BUSTER 2.11.1 REMARK 3 AUTHORS : BRICOGNE,BLANC,BRANDL,FLENSBURG,KELLER, REMARK 3 : PACIOREK,ROVERSI,SHARFF,SMART,VONRHEIN, REMARK 3 : WOMACK,MATTHEWS,TEN EYCK,TRONRUD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 48.15 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 3 NUMBER OF REFLECTIONS : 8996 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 + TEST SET) : 0.250 REMARK 3 R VALUE (WORKING SET) : 0.248 REMARK 3 FREE R VALUE : 0.289 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.750 REMARK 3 FREE R VALUE TEST SET COUNT : 427 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 : 5 REMARK 3 BIN RESOLUTION RANGE HIGH (ANGSTROMS) : 2.40 REMARK 3 BIN RESOLUTION RANGE LOW (ANGSTROMS) : 2.68 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 99.81 REMARK 3 REFLECTIONS IN BIN (WORKING + TEST SET) : 2538 REMARK 3 BIN R VALUE (WORKING + TEST SET) : 0.3688 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 2408 REMARK 3 BIN R VALUE (WORKING SET) : 0.3686 REMARK 3 BIN FREE R VALUE : 0.3728 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 5.12 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 130 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 : 1605 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 34 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 55.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.97 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 8.33410 REMARK 3 B22 (A**2) : -3.11990 REMARK 3 B33 (A**2) : -5.21420 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -3.37310 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 DPI (BLOW EQ-10) BASED ON R VALUE (A) : 0.507 REMARK 3 DPI (BLOW EQ-9) BASED ON FREE R VALUE (A) : 0.294 REMARK 3 DPI (CRUICKSHANK) BASED ON R VALUE (A) : 0.498 REMARK 3 DPI (CRUICKSHANK) BASED ON FREE R VALUE (A) : 0.296 REMARK 3 REMARK 3 REFERENCES: BLOW, D. (2002) ACTA CRYST D58, 792-797 REMARK 3 CRUICKSHANK, D.W.J. (1999) ACTA CRYST D55, 583-601 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.907 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.885 REMARK 3 REMARK 3 NUMBER OF GEOMETRIC FUNCTION TERMS DEFINED : 15 REMARK 3 TERM COUNT WEIGHT FUNCTION. REMARK 3 BOND LENGTHS : 1661 ; 2.000 ; HARMONIC REMARK 3 BOND ANGLES : 2242 ; 2.000 ; HARMONIC REMARK 3 TORSION ANGLES : 618 ; 2.000 ; SINUSOIDAL REMARK 3 TRIGONAL CARBON PLANES : 34 ; 2.000 ; HARMONIC REMARK 3 GENERAL PLANES : 264 ; 5.000 ; HARMONIC REMARK 3 ISOTROPIC THERMAL FACTORS : 1661 ; 20.000 ; HARMONIC REMARK 3 BAD NON-BONDED CONTACTS : NULL ; NULL ; NULL REMARK 3 IMPROPER TORSIONS : NULL ; NULL ; NULL REMARK 3 PSEUDOROTATION ANGLES : NULL ; NULL ; NULL REMARK 3 CHIRAL IMPROPER TORSION : 197 ; 5.000 ; SEMIHARMONIC REMARK 3 SUM OF OCCUPANCIES : NULL ; NULL ; NULL REMARK 3 UTILITY DISTANCES : NULL ; NULL ; NULL REMARK 3 UTILITY ANGLES : NULL ; NULL ; NULL REMARK 3 UTILITY TORSION : NULL ; NULL ; NULL REMARK 3 IDEAL-DIST CONTACT TERM : 1710 ; 4.000 ; SEMIHARMONIC REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.008 REMARK 3 BOND ANGLES (DEGREES) : 1.06 REMARK 3 PEPTIDE OMEGA TORSION ANGLES (DEGREES) : 2.44 REMARK 3 OTHER TORSION ANGLES (DEGREES) : 23.33 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 5MR9 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 21-DEC-16. REMARK 100 THE DEPOSITION ID IS D_1200002886. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 05-SEP-11 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 10.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ESRF REMARK 200 BEAMLINE : ID23-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.992 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 4 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 8997 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.400 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 6.7000 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 <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: PHASER REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 49.74 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.45 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40% MPD AND 100 MM CAPS PH 10.5., REMARK 280 VAPOR DIFFUSION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 4110 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 11660 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -8.0 KCAL/MOL 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 ALA A 96 REMARK 465 ARG A 97 REMARK 465 LEU A 98 REMARK 465 ALA B 96 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 CYS A 134 58.46 -118.57 REMARK 500 GLU A 135 54.87 -101.46 REMARK 500 ALA A 136 38.64 -99.05 REMARK 500 ALA A 137 128.95 62.72 REMARK 500 ARG A 156 91.07 -55.71 REMARK 500 ARG B 101 122.61 108.06 REMARK 500 ARG B 101 124.00 105.99 REMARK 500 ARG B 156 -9.43 82.06 REMARK 500 VAL B 159 116.88 54.37 REMARK 500 REMARK 500 REMARK: NULL DBREF 5MR9 A 96 197 UNP Q99748 NRTN_HUMAN 96 197 DBREF 5MR9 B 96 197 UNP Q99748 NRTN_HUMAN 96 197 SEQRES 1 A 102 ALA ARG LEU GLY ALA ARG PRO CYS GLY LEU ARG GLU LEU SEQRES 2 A 102 GLU VAL ARG VAL SER GLU LEU GLY LEU GLY TYR ALA SER SEQRES 3 A 102 ASP GLU THR VAL LEU PHE ARG TYR CYS ALA GLY ALA CYS SEQRES 4 A 102 GLU ALA ALA ALA ARG VAL TYR ASP LEU GLY LEU ARG ARG SEQRES 5 A 102 LEU ARG GLN ARG ARG ARG LEU ARG ARG GLU ARG VAL ARG SEQRES 6 A 102 ALA GLN PRO CYS CYS ARG PRO THR ALA TYR GLU ASP GLU SEQRES 7 A 102 VAL SER PHE LEU ASP ALA HIS SER ARG TYR HIS THR VAL SEQRES 8 A 102 HIS GLU LEU SER ALA ARG GLU CYS ALA CYS VAL SEQRES 1 B 102 ALA ARG LEU GLY ALA ARG PRO CYS GLY LEU ARG GLU LEU SEQRES 2 B 102 GLU VAL ARG VAL SER GLU LEU GLY LEU GLY TYR ALA SER SEQRES 3 B 102 ASP GLU THR VAL LEU PHE ARG TYR CYS ALA GLY ALA CYS SEQRES 4 B 102 GLU ALA ALA ALA ARG VAL TYR ASP LEU GLY LEU ARG ARG SEQRES 5 B 102 LEU ARG GLN ARG ARG ARG LEU ARG ARG GLU ARG VAL ARG SEQRES 6 B 102 ALA GLN PRO CYS CYS ARG PRO THR ALA TYR GLU ASP GLU SEQRES 7 B 102 VAL SER PHE LEU ASP ALA HIS SER ARG TYR HIS THR VAL SEQRES 8 B 102 HIS GLU LEU SER ALA ARG GLU CYS ALA CYS VAL FORMUL 3 HOH *34(H2 O) HELIX 1 AA1 SER A 113 GLY A 116 5 4 HELIX 2 AA2 ARG A 139 ARG A 151 1 13 HELIX 3 AA3 SER B 113 GLY B 116 5 4 HELIX 4 AA4 ARG B 139 ARG B 151 1 13 SHEET 1 AA1 2 GLY A 104 ARG A 111 0 SHEET 2 AA1 2 THR A 124 ALA A 131 -1 O PHE A 127 N LEU A 108 SHEET 1 AA2 2 CYS A 165 TYR A 170 0 SHEET 2 AA2 2 ALA A 191 CYS A 196 -1 O ARG A 192 N ALA A 169 SHEET 1 AA3 2 VAL A 174 LEU A 177 0 SHEET 2 AA3 2 TYR A 183 VAL A 186 -1 O HIS A 184 N PHE A 176 SHEET 1 AA4 2 GLY B 104 ARG B 111 0 SHEET 2 AA4 2 THR B 124 ALA B 131 -1 O PHE B 127 N LEU B 108 SHEET 1 AA5 2 CYS B 165 TYR B 170 0 SHEET 2 AA5 2 ALA B 191 CYS B 196 -1 O ARG B 192 N ALA B 169 SHEET 1 AA6 2 GLU B 173 LEU B 177 0 SHEET 2 AA6 2 TYR B 183 HIS B 187 -1 O VAL B 186 N VAL B 174 SSBOND 1 CYS A 103 CYS A 165 1555 1555 2.04 SSBOND 2 CYS A 130 CYS A 194 1555 1555 2.02 SSBOND 3 CYS B 103 CYS B 165 1555 1555 2.03 SSBOND 4 CYS B 130 CYS B 194 1555 1555 2.03 SSBOND 5 CYS B 134 CYS B 196 1555 1555 2.04 CISPEP 1 ALA B 136 ALA B 137 0 -2.60 CRYST1 58.080 32.750 61.910 90.00 107.06 90.00 P 1 2 1 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 0.017218 0.000000 0.005284 0.00000 SCALE2 0.000000 0.030534 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016896 0.00000