PDB Short entry for 2D9Q HEADER SIGNALING PROTEIN/CYTOKINE 12-DEC-05 2D9Q TITLE CRYSTAL STRUCTURE OF THE HUMAN GCSF-RECEPTOR SIGNALING COMPLEX COMPND MOL_ID: 1; COMPND 2 MOLECULE: CSF3; COMPND 3 CHAIN: A; COMPND 4 FRAGMENT: RESIDUES 1-174; COMPND 5 SYNONYM: GRANULOCYTE COLONY STIMULATING FACTOR, GCSF; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: GRANULOCYTE COLONY-STIMULATING FACTOR RECEPTOR; COMPND 9 CHAIN: B; COMPND 10 FRAGMENT: IG-CRH DOMAIN; COMPND 11 SYNONYM: G-CSF-R, CD114 ANTIGEN, GCSF-R; COMPND 12 ENGINEERED: YES; COMPND 13 MUTATION: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 MOL_ID: 2; SOURCE 9 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 10 ORGANISM_COMMON: HUMAN; SOURCE 11 ORGANISM_TAXID: 9606; SOURCE 12 EXPRESSION_SYSTEM: SPODOPTERA FRUGIPERDA; SOURCE 13 EXPRESSION_SYSTEM_COMMON: FALL ARMYWORM; SOURCE 14 EXPRESSION_SYSTEM_TAXID: 7108; SOURCE 15 EXPRESSION_SYSTEM_CELL_LINE: SF9; SOURCE 16 EXPRESSION_SYSTEM_VECTOR_TYPE: BACUROVIRUS KEYWDS CYTOKINE, LIGAND-RECEPTOR COMPLEX, SIGNALING PROTEIN-CYTOKINE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR T.TAMADA,R.KUROKI REVDAT 7 25-OCT-23 2D9Q 1 REMARK REVDAT 6 10-NOV-21 2D9Q 1 SEQADV HETSYN REVDAT 5 29-JUL-20 2D9Q 1 COMPND REMARK SEQADV HETNAM REVDAT 5 2 1 LINK SITE ATOM REVDAT 4 13-JUL-11 2D9Q 1 VERSN REVDAT 3 24-FEB-09 2D9Q 1 VERSN REVDAT 2 20-JUN-06 2D9Q 1 JRNL REVDAT 1 07-FEB-06 2D9Q 0 JRNL AUTH T.TAMADA,E.HONJO,Y.MAEDA,T.OKAMOTO,M.ISHIBASHI,M.TOKUNAGA, JRNL AUTH 2 R.KUROKI JRNL TITL HOMODIMERIC CROSS-OVER STRUCTURE OF THE HUMAN GRANULOCYTE JRNL TITL 2 COLONY-STIMULATING FACTOR (GCSF) RECEPTOR SIGNALING COMPLEX JRNL REF PROC.NATL.ACAD.SCI.USA V. 103 3135 2006 JRNL REFN ISSN 0027-8424 JRNL PMID 16492764 JRNL DOI 10.1073/PNAS.0511264103 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH E.HONJO,T.TAMADA,Y.MEADA,T.KOSHIBA,Y.MATSUKURA,T.OKAMOTO, REMARK 1 AUTH 2 M.ISHIBASHI,M.TOKUNAGA,R.KUROKI REMARK 1 TITL CRYSTALLIZATION OF A 2:2 COMPLEX OF GRANULOCYTE-COLONY REMARK 1 TITL 2 STIMULATING FACTOR (GCSF) WITH THE LIGAND-BINDING REGION OF REMARK 1 TITL 3 THE GCSF RECEPTOR REMARK 1 REF ACTA CRYSTALLOGR.,SECT.F V. 61 788 2005 REMARK 1 REFN ESSN 1744-3091 REMARK 1 DOI 10.1107/S1744309105023080 REMARK 1 REFERENCE 2 REMARK 1 AUTH S.MINE,T.KOSHIBA,E.HONJO,T.OKAMOTO,T.TAMADA,Y.MAEDA, REMARK 1 AUTH 2 Y.MATSUKURA,A.HORIE,M.ISHIBASHI,M.SATO,M.AZUMA,M.TOKUNAGA, REMARK 1 AUTH 3 K.NITTA,R.KUROKI REMARK 1 TITL THERMODYNAMIC ANALYSIS OF THE ACTIVATION MECHANISM OF THE REMARK 1 TITL 2 GCSF RECEPTOR INDUCED BY LIGAND BINDING REMARK 1 REF BIOCHEMISTRY V. 43 2458 2004 REMARK 1 REFN ISSN 0006-2960 REMARK 1 PMID 14992583 REMARK 1 DOI 10.1021/BI0356855 REMARK 2 REMARK 2 RESOLUTION. 2.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.19 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 20.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 91.2 REMARK 3 NUMBER OF REFLECTIONS : 23837 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) : 0.253 REMARK 3 R VALUE (WORKING SET) : 0.251 REMARK 3 FREE R VALUE : 0.284 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1264 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.87 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1494 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.4390 REMARK 3 BIN FREE R VALUE SET COUNT : 60 REMARK 3 BIN FREE R VALUE : 0.4390 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3605 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 28 REMARK 3 SOLVENT ATOMS : 14 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 43.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 68.03 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 3.32000 REMARK 3 B22 (A**2) : 3.32000 REMARK 3 B33 (A**2) : -4.98000 REMARK 3 B12 (A**2) : 1.66000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.464 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.327 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.302 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 18.388 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.914 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.895 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3738 ; 0.037 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 3371 ; 0.001 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5105 ; 2.975 ; 1.980 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7893 ; 1.182 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 464 ; 8.748 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): NULL ; NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 576 ; 0.143 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4085 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 660 ; 0.004 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 1037 ; 0.314 ; 0.300 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 4287 ; 0.296 ; 0.300 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 2406 ; 0.126 ; 0.500 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 169 ; 0.241 ; 0.500 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 17 ; 0.350 ; 0.300 REMARK 3 SYMMETRY VDW OTHERS (A): 54 ; 0.308 ; 0.300 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.347 ; 0.500 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 2340 ; 2.089 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3773 ; 3.667 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1398 ; 1.878 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1332 ; 3.209 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : BABINET MODEL WITH MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2D9Q COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 15-DEC-05. REMARK 100 THE DEPOSITION ID IS D_1000025161. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 19-FEB-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.8 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SPRING-8 REMARK 200 BEAMLINE : BL38B1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0000 REMARK 200 MONOCHROMATOR : SI(111) 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 : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 25214 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.800 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 (%) : 91.0 REMARK 200 DATA REDUNDANCY : 5.900 REMARK 200 R MERGE (I) : 0.05800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 20.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.90 REMARK 200 COMPLETENESS FOR SHELL (%) : 78.0 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.35500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MIR AND MOLECULAR REMARK 200 REPLACEMENT REMARK 200 SOFTWARE USED: MLPHARE, SHARP, PHASER REMARK 200 STARTING MODEL: PDB ENTRY 1CD9 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 76.20 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 5.17 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M AMMONIUM PHOSPHATE, PH 4.8, VAPOR REMARK 280 DIFFUSION, HANGING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 32 2 1 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 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+1/3 REMARK 290 6555 -X,-X+Y,-Z+2/3 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 70.31200 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 35.15600 REMARK 290 SMTRY1 4 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 4 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 5 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 5 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 35.15600 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 70.31200 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: TETRAMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C 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 350 BIOMT1 2 1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 35.15600 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 THR A 1 REMARK 465 PRO A 2 REMARK 465 LEU A 3 REMARK 465 GLY A 4 REMARK 465 PRO A 5 REMARK 465 ALA A 6 REMARK 465 GLU B 2 REMARK 465 SER B 215 REMARK 465 PRO B 216 REMARK 465 GLU B 217 REMARK 465 ALA B 218 REMARK 465 ALA B 219 REMARK 465 PRO B 220 REMARK 465 PRO B 221 REMARK 465 ARG B 309 REMARK 465 ALA B 310 REMARK 465 ALA B 311 REMARK 465 ALA B 312 REMARK 465 PRO B 313 REMARK 465 ARG B 314 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 PRO B 276 CG2 THR B 278 1.99 REMARK 500 O ASP B 33 N GLU B 35 2.12 REMARK 500 O SER A 159 N LEU A 161 2.19 REMARK 500 NE2 GLN A 20 O HOH A 176 2.19 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS 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,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3) 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 RES CSSEQI ATM2 DEVIATION REMARK 500 TYR A 39 CE1 TYR A 39 CZ -0.082 REMARK 500 PHE A 113 CE2 PHE A 113 CD2 -0.123 REMARK 500 ARG A 147 CG ARG A 147 CD 0.183 REMARK 500 ARG A 166 CB ARG A 166 CG 0.178 REMARK 500 THR B 146 CA THR B 146 CB 0.160 REMARK 500 MET B 208 CB MET B 208 CG 0.227 REMARK 500 MET B 208 CG MET B 208 SD 0.374 REMARK 500 TRP B 230 CE3 TRP B 230 CZ3 -0.102 REMARK 500 REMARK 500 REMARK: NULL 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 LEU A 15 CB - CG - CD1 ANGL. DEV. = -10.3 DEGREES REMARK 500 LEU A 69 CB - CA - C ANGL. DEV. = 11.9 DEGREES REMARK 500 VAL A 151 CB - CA - C ANGL. DEV. = -11.6 DEGREES REMARK 500 CYS B 3 CA - CB - SG ANGL. DEV. = -11.5 DEGREES REMARK 500 ASP B 17 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 ILE B 118 CG1 - CB - CG2 ANGL. DEV. = -17.9 DEGREES REMARK 500 PRO B 123 N - CD - CG ANGL. DEV. = -12.1 DEGREES REMARK 500 ASP B 153 CB - CG - OD2 ANGL. DEV. = 6.2 DEGREES REMARK 500 GLU B 183 OE1 - CD - OE2 ANGL. DEV. = 7.4 DEGREES REMARK 500 ASP B 200 CB - CG - OD1 ANGL. DEV. = 9.6 DEGREES REMARK 500 MET B 208 CB - CG - SD ANGL. DEV. = 19.6 DEGREES REMARK 500 ARG B 251 NE - CZ - NH1 ANGL. DEV. = 3.1 DEGREES REMARK 500 LEU B 258 CA - CB - CG ANGL. DEV. = 17.3 DEGREES REMARK 500 LEU B 264 CB - CG - CD1 ANGL. DEV. = -13.4 DEGREES REMARK 500 PRO B 290 N - CD - CG ANGL. DEV. = -13.2 DEGREES REMARK 500 ARG B 305 NE - CZ - NH1 ANGL. DEV. = 4.3 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 TYR A 39 0.13 -160.10 REMARK 500 LEU A 41 76.64 -100.62 REMARK 500 GLU A 46 -5.83 -50.20 REMARK 500 SER A 53 -18.62 -44.79 REMARK 500 LEU A 61 64.16 -161.07 REMARK 500 PRO A 65 -46.41 -24.68 REMARK 500 SER A 66 27.90 -174.36 REMARK 500 ALA A 68 -144.30 169.75 REMARK 500 LEU A 71 -107.16 -62.17 REMARK 500 ALA A 72 159.89 -18.37 REMARK 500 LEU A 78 -98.70 -28.43 REMARK 500 HIS A 79 -60.10 -11.17 REMARK 500 ILE A 95 -82.04 64.21 REMARK 500 LEU A 99 -68.31 -98.34 REMARK 500 ILE A 117 -60.41 -92.68 REMARK 500 GLN A 120 -36.90 -32.28 REMARK 500 PRO A 128 147.02 -28.68 REMARK 500 PRO A 132 152.00 -44.51 REMARK 500 PRO A 138 170.98 -59.06 REMARK 500 ALA A 139 -84.55 -58.35 REMARK 500 LEU A 157 -38.79 -37.49 REMARK 500 PHE A 160 -22.88 -35.31 REMARK 500 VAL A 167 -3.80 -51.94 REMARK 500 LEU A 171 -15.40 -47.66 REMARK 500 SER B 9 -70.60 -66.76 REMARK 500 LEU B 15 -82.22 17.66 REMARK 500 SER B 30 118.45 164.36 REMARK 500 HIS B 31 -81.04 -59.01 REMARK 500 PRO B 34 -26.46 -2.71 REMARK 500 GLU B 35 -64.94 -20.49 REMARK 500 LEU B 42 46.78 -109.32 REMARK 500 PRO B 48 -167.81 -49.00 REMARK 500 GLN B 53 -141.40 -82.42 REMARK 500 SER B 56 -83.76 103.98 REMARK 500 THR B 59 138.60 -30.52 REMARK 500 GLN B 60 61.40 -105.29 REMARK 500 PRO B 67 -74.50 -63.82 REMARK 500 LEU B 69 96.00 -58.27 REMARK 500 ASN B 70 31.48 -99.92 REMARK 500 LEU B 80 -154.29 -96.29 REMARK 500 ASN B 84 77.33 -105.25 REMARK 500 SER B 85 137.32 176.25 REMARK 500 ASN B 105 42.21 79.52 REMARK 500 PRO B 125 130.03 -34.63 REMARK 500 PRO B 130 105.37 -59.21 REMARK 500 SER B 140 -162.19 -128.22 REMARK 500 CYS B 144 -8.24 57.30 REMARK 500 THR B 146 99.44 -56.05 REMARK 500 GLN B 147 123.86 -39.29 REMARK 500 ASP B 158 108.05 -16.91 REMARK 500 REMARK 500 THIS ENTRY HAS 60 RAMACHANDRAN OUTLIERS. REMARK 500 REMARK 500 REMARK: NULL DBREF 2D9Q A 1 174 UNP P09919 CSF3_HUMAN 31 204 DBREF 2D9Q B 2 309 UNP Q99062 CSF3R_HUMAN 25 332 SEQADV 2D9Q SER B 79 UNP Q99062 CYS 102 ENGINEERED MUTATION SEQADV 2D9Q SER B 164 UNP Q99062 CYS 187 ENGINEERED MUTATION SEQADV 2D9Q SER B 229 UNP Q99062 CYS 252 ENGINEERED MUTATION SEQADV 2D9Q ALA B 310 UNP Q99062 CLONING ARTIFACT SEQADV 2D9Q ALA B 311 UNP Q99062 CLONING ARTIFACT SEQADV 2D9Q ALA B 312 UNP Q99062 CLONING ARTIFACT SEQADV 2D9Q PRO B 313 UNP Q99062 CLONING ARTIFACT SEQADV 2D9Q ARG B 314 UNP Q99062 CLONING ARTIFACT SEQRES 1 A 174 THR PRO LEU GLY PRO ALA SER SER LEU PRO GLN SER PHE SEQRES 2 A 174 LEU LEU LYS CYS LEU GLU GLN VAL ARG LYS ILE GLN GLY SEQRES 3 A 174 ASP GLY ALA ALA LEU GLN GLU LYS LEU CYS ALA THR TYR SEQRES 4 A 174 LYS LEU CYS HIS PRO GLU GLU LEU VAL LEU LEU GLY HIS SEQRES 5 A 174 SER LEU GLY ILE PRO TRP ALA PRO LEU SER SER CYS PRO SEQRES 6 A 174 SER GLN ALA LEU GLN LEU ALA GLY CYS LEU SER GLN LEU SEQRES 7 A 174 HIS SER GLY LEU PHE LEU TYR GLN GLY LEU LEU GLN ALA SEQRES 8 A 174 LEU GLU GLY ILE SER PRO GLU LEU GLY PRO THR LEU ASP SEQRES 9 A 174 THR LEU GLN LEU ASP VAL ALA ASP PHE ALA THR THR ILE SEQRES 10 A 174 TRP GLN GLN MET GLU GLU LEU GLY MET ALA PRO ALA LEU SEQRES 11 A 174 GLN PRO THR GLN GLY ALA MET PRO ALA PHE ALA SER ALA SEQRES 12 A 174 PHE GLN ARG ARG ALA GLY GLY VAL LEU VAL ALA SER HIS SEQRES 13 A 174 LEU GLN SER PHE LEU GLU VAL SER TYR ARG VAL LEU ARG SEQRES 14 A 174 HIS LEU ALA GLN PRO SEQRES 1 B 313 GLU CYS GLY HIS ILE SER VAL SER ALA PRO ILE VAL HIS SEQRES 2 B 313 LEU GLY ASP PRO ILE THR ALA SER CYS ILE ILE LYS GLN SEQRES 3 B 313 ASN CYS SER HIS LEU ASP PRO GLU PRO GLN ILE LEU TRP SEQRES 4 B 313 ARG LEU GLY ALA GLU LEU GLN PRO GLY GLY ARG GLN GLN SEQRES 5 B 313 ARG LEU SER ASP GLY THR GLN GLU SER ILE ILE THR LEU SEQRES 6 B 313 PRO HIS LEU ASN HIS THR GLN ALA PHE LEU SER CYS SER SEQRES 7 B 313 LEU ASN TRP GLY ASN SER LEU GLN ILE LEU ASP GLN VAL SEQRES 8 B 313 GLU LEU ARG ALA GLY TYR PRO PRO ALA ILE PRO HIS ASN SEQRES 9 B 313 LEU SER CYS LEU MET ASN LEU THR THR SER SER LEU ILE SEQRES 10 B 313 CYS GLN TRP GLU PRO GLY PRO GLU THR HIS LEU PRO THR SEQRES 11 B 313 SER PHE THR LEU LYS SER PHE LYS SER ARG GLY ASN CYS SEQRES 12 B 313 GLN THR GLN GLY ASP SER ILE LEU ASP CYS VAL PRO LYS SEQRES 13 B 313 ASP GLY GLN SER HIS CYS SER ILE PRO ARG LYS HIS LEU SEQRES 14 B 313 LEU LEU TYR GLN ASN MET GLY ILE TRP VAL GLN ALA GLU SEQRES 15 B 313 ASN ALA LEU GLY THR SER MET SER PRO GLN LEU CYS LEU SEQRES 16 B 313 ASP PRO MET ASP VAL VAL LYS LEU GLU PRO PRO MET LEU SEQRES 17 B 313 ARG THR MET ASP PRO SER PRO GLU ALA ALA PRO PRO GLN SEQRES 18 B 313 ALA GLY CYS LEU GLN LEU SER TRP GLU PRO TRP GLN PRO SEQRES 19 B 313 GLY LEU HIS ILE ASN GLN LYS CYS GLU LEU ARG HIS LYS SEQRES 20 B 313 PRO GLN ARG GLY GLU ALA SER TRP ALA LEU VAL GLY PRO SEQRES 21 B 313 LEU PRO LEU GLU ALA LEU GLN TYR GLU LEU CYS GLY LEU SEQRES 22 B 313 LEU PRO ALA THR ALA TYR THR LEU GLN ILE ARG CYS ILE SEQRES 23 B 313 ARG TRP PRO LEU PRO GLY HIS TRP SER ASP TRP SER PRO SEQRES 24 B 313 SER LEU GLU LEU ARG THR THR GLU ARG ALA ALA ALA PRO SEQRES 25 B 313 ARG MODRES 2D9Q ASN B 111 ASN GLYCOSYLATION SITE HET NAG C 1 14 HET NAG C 2 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE FORMUL 3 NAG 2(C8 H15 N O6) FORMUL 4 HOH *14(H2 O) HELIX 1 1 PRO A 10 ALA A 37 1 28 HELIX 2 2 LEU A 47 GLY A 55 1 9 HELIX 3 3 GLY A 73 ALA A 91 1 19 HELIX 4 4 LEU A 99 GLU A 123 1 25 HELIX 5 5 SER A 142 HIS A 170 1 29 HELIX 6 6 LYS B 168 LEU B 170 5 3 HELIX 7 7 ASP B 197 ASP B 200 5 4 HELIX 8 8 TRP B 233 LEU B 237 5 5 SHEET 1 A 4 ILE B 6 VAL B 8 0 SHEET 2 A 4 ILE B 19 CYS B 23 -1 O SER B 22 N SER B 7 SHEET 3 A 4 SER B 62 LEU B 66 -1 O SER B 62 N CYS B 23 SHEET 4 A 4 ARG B 51 GLN B 52 -1 N ARG B 51 O ILE B 63 SHEET 1 B 4 ILE B 12 VAL B 13 0 SHEET 2 B 4 LEU B 86 ALA B 96 1 O ARG B 95 N VAL B 13 SHEET 3 B 4 GLN B 73 ASN B 81 -1 N ALA B 74 O LEU B 94 SHEET 4 B 4 LEU B 39 ARG B 41 -1 N LEU B 39 O SER B 79 SHEET 1 C 4 HIS B 162 PRO B 166 0 SHEET 2 C 4 SER B 116 GLU B 122 -1 N LEU B 117 O ILE B 165 SHEET 3 C 4 HIS B 104 ASN B 111 -1 N LEU B 109 O ILE B 118 SHEET 4 C 4 VAL B 202 LYS B 203 1 O LYS B 203 N MET B 110 SHEET 1 D 4 ILE B 151 CYS B 154 0 SHEET 2 D 4 SER B 132 LYS B 139 -1 N SER B 137 O LEU B 152 SHEET 3 D 4 MET B 176 ASN B 184 -1 O GLN B 181 N THR B 134 SHEET 4 D 4 GLY B 187 MET B 190 -1 O SER B 189 N ALA B 182 SHEET 1 E 4 ILE B 151 CYS B 154 0 SHEET 2 E 4 SER B 132 LYS B 139 -1 N SER B 137 O LEU B 152 SHEET 3 E 4 MET B 176 ASN B 184 -1 O GLN B 181 N THR B 134 SHEET 4 E 4 LEU B 194 LEU B 196 -1 O LEU B 194 N ILE B 178 SHEET 1 F 3 MET B 208 THR B 211 0 SHEET 2 F 3 LEU B 226 GLU B 231 -1 O SER B 229 N ARG B 210 SHEET 3 F 3 ALA B 266 LEU B 271 -1 O TYR B 269 N LEU B 228 SHEET 1 G 4 ALA B 257 LEU B 262 0 SHEET 2 G 4 GLN B 241 PRO B 249 -1 N CYS B 243 O LEU B 262 SHEET 3 G 4 TYR B 280 ARG B 288 -1 O ILE B 287 N LYS B 242 SHEET 4 G 4 LEU B 302 LEU B 304 -1 O LEU B 304 N TYR B 280 SSBOND 1 CYS A 36 CYS A 42 1555 1555 2.25 SSBOND 2 CYS A 64 CYS A 74 1555 1555 2.09 SSBOND 3 CYS B 3 CYS B 29 1555 1555 2.09 SSBOND 4 CYS B 23 CYS B 78 1555 1555 2.07 SSBOND 5 CYS B 108 CYS B 119 1555 1555 2.21 SSBOND 6 CYS B 144 CYS B 195 1555 1555 2.11 SSBOND 7 CYS B 154 CYS B 163 1555 1555 2.20 SSBOND 8 CYS B 225 CYS B 272 1555 1555 2.12 SSBOND 9 CYS B 243 CYS B 286 1555 1555 2.16 LINK ND2 ASN B 111 C1 NAG C 1 1555 1555 1.43 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.47 CRYST1 134.777 134.777 105.468 90.00 90.00 120.00 P 32 2 1 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 0.007420 0.004284 0.000000 0.00000 SCALE2 0.000000 0.008567 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009482 0.00000