PDB Short entry for 4DKD HEADER CYTOKINE/TRANSFERASE 03-FEB-12 4DKD TITLE CRYSTAL STRUCTURE OF HUMAN INTERLEUKIN-34 BOUND TO HUMAN CSF-1R COMPND MOL_ID: 1; COMPND 2 MOLECULE: INTERLEUKIN-34; COMPND 3 CHAIN: A, B; COMPND 4 FRAGMENT: ACTIVE CORE, UNP RESIDUES 21-193; COMPND 5 SYNONYM: IL-34; COMPND 6 ENGINEERED: YES; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: MACROPHAGE COLONY-STIMULATING FACTOR 1 RECEPTOR; COMPND 9 CHAIN: C; COMPND 10 FRAGMENT: D1-D3, UNP RESIDUES 20-299; COMPND 11 SYNONYM: CSF-1 RECEPTOR, CSF-1-R, CSF-1R, M-CSF-R, PROTO-ONCOGENE C- COMPND 12 FMS; COMPND 13 EC: 2.7.10.1; COMPND 14 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: IL34, C16ORF77; SOURCE 6 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 8 EXPRESSION_SYSTEM_CELL_LINE: TNI PRO; SOURCE 9 MOL_ID: 2; SOURCE 10 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 11 ORGANISM_COMMON: HUMAN; SOURCE 12 ORGANISM_TAXID: 9606; SOURCE 13 GENE: CSF1R, FMS; SOURCE 14 EXPRESSION_SYSTEM: TRICHOPLUSIA NI; SOURCE 15 EXPRESSION_SYSTEM_TAXID: 7111; SOURCE 16 EXPRESSION_SYSTEM_CELL_LINE: TNI PRO KEYWDS DIMERIC FOUR-HELIX BUNDLE CYTOKINE, RECEPTOR TYROSINE KINASE, KEYWDS 2 GLYCOSYLATION, CYTOKINE-TRANSFERASE COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR X.MA,J.F.BAZAN,M.A.STAROVASNIK REVDAT 3 29-JUL-20 4DKD 1 COMPND REMARK SEQADV HETNAM REVDAT 3 2 1 LINK SITE ATOM REVDAT 2 25-APR-12 4DKD 1 JRNL REVDAT 1 11-APR-12 4DKD 0 JRNL AUTH X.MA,W.Y.LIN,Y.CHEN,S.STAWICKI,K.MUKHYALA,Y.WU,F.MARTIN, JRNL AUTH 2 J.F.BAZAN,M.A.STAROVASNIK JRNL TITL STRUCTURAL BASIS FOR THE DUAL RECOGNITION OF HELICAL JRNL TITL 2 CYTOKINES IL-34 AND CSF-1 BY CSF-1R. JRNL REF STRUCTURE V. 20 676 2012 JRNL REFN ISSN 0969-2126 JRNL PMID 22483114 JRNL DOI 10.1016/J.STR.2012.02.010 REMARK 2 REMARK 2 RESOLUTION. 3.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0109 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) : 3.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.0 REMARK 3 NUMBER OF REFLECTIONS : 20213 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) : 0.254 REMARK 3 R VALUE (WORKING SET) : 0.252 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1090 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) : 3.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 3.08 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1334 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.75 REMARK 3 BIN R VALUE (WORKING SET) : 0.3820 REMARK 3 BIN FREE R VALUE SET COUNT : 84 REMARK 3 BIN FREE R VALUE : 0.4230 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4722 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 134 REMARK 3 SOLVENT ATOMS : 16 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 97.37 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.04000 REMARK 3 B22 (A**2) : 1.04000 REMARK 3 B33 (A**2) : -1.56000 REMARK 3 B12 (A**2) : 0.52000 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): 2.003 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.431 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.351 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 19.418 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.924 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.903 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4974 ; 0.004 ; 0.020 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 6777 ; 0.991 ; 1.993 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 589 ; 5.459 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 220 ;30.400 ;23.955 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 825 ;15.606 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 34 ;15.421 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 792 ; 0.060 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 3707 ; 0.005 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): NULL ; NULL ; NULL 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): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): NULL ; NULL ; NULL 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): 2967 ; 0.632 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4833 ; 1.141 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 2010 ; 0.604 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1952 ; 1.137 ; 4.500 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 : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN USED IF PRESENT IN REMARK 3 THE INPUT REMARK 4 REMARK 4 4DKD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-FEB-12. REMARK 100 THE DEPOSITION ID IS D_1000070438. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-OCT-10 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : ALS REMARK 200 BEAMLINE : 5.0.2 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 : DOUBLE CRYSTAL SI(111) REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : HKL-2000 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 21502 REMARK 200 RESOLUTION RANGE HIGH (A) : 3.000 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 (%) : 99.8 REMARK 200 DATA REDUNDANCY : 7.600 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06100 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 23.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 3.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 3.11 REMARK 200 COMPLETENESS FOR SHELL (%) : 99.8 REMARK 200 DATA REDUNDANCY IN SHELL : 7.00 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.62700 REMARK 200 <I/SIGMA(I)> FOR SHELL : 2.800 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHASES REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 64.55 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.47 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1M CALCIUM ACETATE, 0.1M MES PH 6.0, REMARK 280 15% PEG 400, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 31 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+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 Y,X,-Z REMARK 290 5555 X-Y,-Y,-Z+2/3 REMARK 290 6555 -X,-X+Y,-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 58.41733 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 116.83467 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 116.83467 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 58.41733 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: TRIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B, C, D, E 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 18 REMARK 465 GLY A 19 REMARK 465 SER A 20 REMARK 465 ASN A 21 REMARK 465 GLU A 22 REMARK 465 PRO A 23 REMARK 465 LEU A 24 REMARK 465 GLU A 25 REMARK 465 MET A 26 REMARK 465 TRP A 27 REMARK 465 PRO A 28 REMARK 465 LEU A 29 REMARK 465 THR A 30 REMARK 465 GLN A 31 REMARK 465 VAL A 193 REMARK 465 GLY A 194 REMARK 465 ASN A 195 REMARK 465 SER A 196 REMARK 465 HIS A 197 REMARK 465 HIS A 198 REMARK 465 HIS A 199 REMARK 465 HIS A 200 REMARK 465 HIS A 201 REMARK 465 HIS A 202 REMARK 465 ALA B 18 REMARK 465 GLY B 19 REMARK 465 SER B 20 REMARK 465 ASN B 21 REMARK 465 GLU B 22 REMARK 465 PRO B 23 REMARK 465 LEU B 24 REMARK 465 GLU B 25 REMARK 465 MET B 26 REMARK 465 TRP B 27 REMARK 465 PRO B 28 REMARK 465 LEU B 29 REMARK 465 THR B 30 REMARK 465 GLN B 31 REMARK 465 ASN B 32 REMARK 465 VAL B 193 REMARK 465 GLY B 194 REMARK 465 ASN B 195 REMARK 465 SER B 196 REMARK 465 HIS B 197 REMARK 465 HIS B 198 REMARK 465 HIS B 199 REMARK 465 HIS B 200 REMARK 465 HIS B 201 REMARK 465 HIS B 202 REMARK 465 ALA C 17 REMARK 465 GLY C 18 REMARK 465 SER C 19 REMARK 465 GLY C 88 REMARK 465 ASP C 89 REMARK 465 PRO C 90 REMARK 465 LEU C 91 REMARK 465 VAL C 296 REMARK 465 GLU C 297 REMARK 465 SER C 298 REMARK 465 ALA C 299 REMARK 465 GLY C 300 REMARK 465 ASN C 301 REMARK 465 SER C 302 REMARK 465 HIS C 303 REMARK 465 HIS C 304 REMARK 465 HIS C 305 REMARK 465 HIS C 306 REMARK 465 HIS C 307 REMARK 465 HIS C 308 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 LEU B 186 OE1 GLN B 189 2.01 REMARK 500 O LEU C 180 O ARG C 184 2.03 REMARK 500 ND2 ASN B 76 C2 NAG E 1 2.06 REMARK 500 O3 BMA B 303 O HOH B 402 2.09 REMARK 500 OE2 GLU A 173 N GLU A 192 2.10 REMARK 500 O HIS C 272 OH TYR C 276 2.13 REMARK 500 NH1 ARG C 214 O ALA C 219 2.17 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 CYS C 224 CA - CB - SG ANGL. DEV. = -11.2 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 ALA A 83 7.50 -68.45 REMARK 500 ASP A 107 1.69 -65.39 REMARK 500 GLU A 111 -18.10 -47.26 REMARK 500 PRO A 152 -170.44 -51.53 REMARK 500 GLN A 189 0.03 -69.73 REMARK 500 LYS B 55 -56.31 -123.00 REMARK 500 ALA B 83 1.70 -65.46 REMARK 500 SER B 86 156.96 -49.61 REMARK 500 VAL B 136 124.24 -33.07 REMARK 500 LEU B 156 -68.75 -109.56 REMARK 500 ALA B 163 -71.29 -46.25 REMARK 500 ASN B 167 -38.61 -39.57 REMARK 500 SER B 184 -5.57 93.75 REMARK 500 PRO C 21 -178.87 -60.37 REMARK 500 SER C 47 141.13 84.40 REMARK 500 SER C 55 -177.31 150.36 REMARK 500 PRO C 56 -162.07 -120.51 REMARK 500 PRO C 126 55.50 -68.62 REMARK 500 ARG C 150 -36.41 97.45 REMARK 500 MET C 181 80.53 48.65 REMARK 500 VAL C 198 -63.38 112.85 REMARK 500 ILE C 199 151.69 63.46 REMARK 500 ARG C 214 151.12 179.56 REMARK 500 ALA C 219 71.14 58.58 REMARK 500 ASN C 240 -119.32 37.39 REMARK 500 MET C 291 145.51 -176.31 REMARK 500 REMARK 500 REMARK: NULL REMARK 610 REMARK 610 MISSING HETEROATOM REMARK 610 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 610 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 610 I=INSERTION CODE): REMARK 610 M RES C SSEQI REMARK 610 BMA A 303 REMARK 610 BMA B 303 DBREF 4DKD A 21 193 UNP Q6ZMJ4 IL34_HUMAN 21 193 DBREF 4DKD B 21 193 UNP Q6ZMJ4 IL34_HUMAN 21 193 DBREF 4DKD C 20 299 UNP P07333 CSF1R_HUMAN 20 299 SEQADV 4DKD ALA A 18 UNP Q6ZMJ4 EXPRESSION TAG SEQADV 4DKD GLY A 19 UNP Q6ZMJ4 EXPRESSION TAG SEQADV 4DKD SER A 20 UNP Q6ZMJ4 EXPRESSION TAG SEQADV 4DKD GLY A 194 UNP Q6ZMJ4 EXPRESSION TAG SEQADV 4DKD ASN A 195 UNP Q6ZMJ4 EXPRESSION TAG SEQADV 4DKD SER A 196 UNP Q6ZMJ4 EXPRESSION TAG SEQADV 4DKD HIS A 197 UNP Q6ZMJ4 EXPRESSION TAG SEQADV 4DKD HIS A 198 UNP Q6ZMJ4 EXPRESSION TAG SEQADV 4DKD HIS A 199 UNP Q6ZMJ4 EXPRESSION TAG SEQADV 4DKD HIS A 200 UNP Q6ZMJ4 EXPRESSION TAG SEQADV 4DKD HIS A 201 UNP Q6ZMJ4 EXPRESSION TAG SEQADV 4DKD HIS A 202 UNP Q6ZMJ4 EXPRESSION TAG SEQADV 4DKD ALA B 18 UNP Q6ZMJ4 EXPRESSION TAG SEQADV 4DKD GLY B 19 UNP Q6ZMJ4 EXPRESSION TAG SEQADV 4DKD SER B 20 UNP Q6ZMJ4 EXPRESSION TAG SEQADV 4DKD GLY B 194 UNP Q6ZMJ4 EXPRESSION TAG SEQADV 4DKD ASN B 195 UNP Q6ZMJ4 EXPRESSION TAG SEQADV 4DKD SER B 196 UNP Q6ZMJ4 EXPRESSION TAG SEQADV 4DKD HIS B 197 UNP Q6ZMJ4 EXPRESSION TAG SEQADV 4DKD HIS B 198 UNP Q6ZMJ4 EXPRESSION TAG SEQADV 4DKD HIS B 199 UNP Q6ZMJ4 EXPRESSION TAG SEQADV 4DKD HIS B 200 UNP Q6ZMJ4 EXPRESSION TAG SEQADV 4DKD HIS B 201 UNP Q6ZMJ4 EXPRESSION TAG SEQADV 4DKD HIS B 202 UNP Q6ZMJ4 EXPRESSION TAG SEQADV 4DKD ALA C 17 UNP P07333 EXPRESSION TAG SEQADV 4DKD GLY C 18 UNP P07333 EXPRESSION TAG SEQADV 4DKD SER C 19 UNP P07333 EXPRESSION TAG SEQADV 4DKD GLY C 300 UNP P07333 EXPRESSION TAG SEQADV 4DKD ASN C 301 UNP P07333 EXPRESSION TAG SEQADV 4DKD SER C 302 UNP P07333 EXPRESSION TAG SEQADV 4DKD HIS C 303 UNP P07333 EXPRESSION TAG SEQADV 4DKD HIS C 304 UNP P07333 EXPRESSION TAG SEQADV 4DKD HIS C 305 UNP P07333 EXPRESSION TAG SEQADV 4DKD HIS C 306 UNP P07333 EXPRESSION TAG SEQADV 4DKD HIS C 307 UNP P07333 EXPRESSION TAG SEQADV 4DKD HIS C 308 UNP P07333 EXPRESSION TAG SEQRES 1 A 185 ALA GLY SER ASN GLU PRO LEU GLU MET TRP PRO LEU THR SEQRES 2 A 185 GLN ASN GLU GLU CYS THR VAL THR GLY PHE LEU ARG ASP SEQRES 3 A 185 LYS LEU GLN TYR ARG SER ARG LEU GLN TYR MET LYS HIS SEQRES 4 A 185 TYR PHE PRO ILE ASN TYR LYS ILE SER VAL PRO TYR GLU SEQRES 5 A 185 GLY VAL PHE ARG ILE ALA ASN VAL THR ARG LEU GLN ARG SEQRES 6 A 185 ALA GLN VAL SER GLU ARG GLU LEU ARG TYR LEU TRP VAL SEQRES 7 A 185 LEU VAL SER LEU SER ALA THR GLU SER VAL GLN ASP VAL SEQRES 8 A 185 LEU LEU GLU GLY HIS PRO SER TRP LYS TYR LEU GLN GLU SEQRES 9 A 185 VAL GLU THR LEU LEU LEU ASN VAL GLN GLN GLY LEU THR SEQRES 10 A 185 ASP VAL GLU VAL SER PRO LYS VAL GLU SER VAL LEU SER SEQRES 11 A 185 LEU LEU ASN ALA PRO GLY PRO ASN LEU LYS LEU VAL ARG SEQRES 12 A 185 PRO LYS ALA LEU LEU ASP ASN CYS PHE ARG VAL MET GLU SEQRES 13 A 185 LEU LEU TYR CYS SER CYS CYS LYS GLN SER SER VAL LEU SEQRES 14 A 185 ASN TRP GLN ASP CYS GLU VAL GLY ASN SER HIS HIS HIS SEQRES 15 A 185 HIS HIS HIS SEQRES 1 B 185 ALA GLY SER ASN GLU PRO LEU GLU MET TRP PRO LEU THR SEQRES 2 B 185 GLN ASN GLU GLU CYS THR VAL THR GLY PHE LEU ARG ASP SEQRES 3 B 185 LYS LEU GLN TYR ARG SER ARG LEU GLN TYR MET LYS HIS SEQRES 4 B 185 TYR PHE PRO ILE ASN TYR LYS ILE SER VAL PRO TYR GLU SEQRES 5 B 185 GLY VAL PHE ARG ILE ALA ASN VAL THR ARG LEU GLN ARG SEQRES 6 B 185 ALA GLN VAL SER GLU ARG GLU LEU ARG TYR LEU TRP VAL SEQRES 7 B 185 LEU VAL SER LEU SER ALA THR GLU SER VAL GLN ASP VAL SEQRES 8 B 185 LEU LEU GLU GLY HIS PRO SER TRP LYS TYR LEU GLN GLU SEQRES 9 B 185 VAL GLU THR LEU LEU LEU ASN VAL GLN GLN GLY LEU THR SEQRES 10 B 185 ASP VAL GLU VAL SER PRO LYS VAL GLU SER VAL LEU SER SEQRES 11 B 185 LEU LEU ASN ALA PRO GLY PRO ASN LEU LYS LEU VAL ARG SEQRES 12 B 185 PRO LYS ALA LEU LEU ASP ASN CYS PHE ARG VAL MET GLU SEQRES 13 B 185 LEU LEU TYR CYS SER CYS CYS LYS GLN SER SER VAL LEU SEQRES 14 B 185 ASN TRP GLN ASP CYS GLU VAL GLY ASN SER HIS HIS HIS SEQRES 15 B 185 HIS HIS HIS SEQRES 1 C 292 ALA GLY SER ILE PRO VAL ILE GLU PRO SER VAL PRO GLU SEQRES 2 C 292 LEU VAL VAL LYS PRO GLY ALA THR VAL THR LEU ARG CYS SEQRES 3 C 292 VAL GLY ASN GLY SER VAL GLU TRP ASP GLY PRO PRO SER SEQRES 4 C 292 PRO HIS TRP THR LEU TYR SER ASP GLY SER SER SER ILE SEQRES 5 C 292 LEU SER THR ASN ASN ALA THR PHE GLN ASN THR GLY THR SEQRES 6 C 292 TYR ARG CYS THR GLU PRO GLY ASP PRO LEU GLY GLY SER SEQRES 7 C 292 ALA ALA ILE HIS LEU TYR VAL LYS ASP PRO ALA ARG PRO SEQRES 8 C 292 TRP ASN VAL LEU ALA GLN GLU VAL VAL VAL PHE GLU ASP SEQRES 9 C 292 GLN ASP ALA LEU LEU PRO CYS LEU LEU THR ASP PRO VAL SEQRES 10 C 292 LEU GLU ALA GLY VAL SER LEU VAL ARG VAL ARG GLY ARG SEQRES 11 C 292 PRO LEU MET ARG HIS THR ASN TYR SER PHE SER PRO TRP SEQRES 12 C 292 HIS GLY PHE THR ILE HIS ARG ALA LYS PHE ILE GLN SER SEQRES 13 C 292 GLN ASP TYR GLN CYS SER ALA LEU MET GLY GLY ARG LYS SEQRES 14 C 292 VAL MET SER ILE SER ILE ARG LEU LYS VAL GLN LYS VAL SEQRES 15 C 292 ILE PRO GLY PRO PRO ALA LEU THR LEU VAL PRO ALA GLU SEQRES 16 C 292 LEU VAL ARG ILE ARG GLY GLU ALA ALA GLN ILE VAL CYS SEQRES 17 C 292 SER ALA SER SER VAL ASP VAL ASN PHE ASP VAL PHE LEU SEQRES 18 C 292 GLN HIS ASN ASN THR LYS LEU ALA ILE PRO GLN GLN SER SEQRES 19 C 292 ASP PHE HIS ASN ASN ARG TYR GLN LYS VAL LEU THR LEU SEQRES 20 C 292 ASN LEU ASP GLN VAL ASP PHE GLN HIS ALA GLY ASN TYR SEQRES 21 C 292 SER CYS VAL ALA SER ASN VAL GLN GLY LYS HIS SER THR SEQRES 22 C 292 SER MET PHE PHE ARG VAL VAL GLU SER ALA GLY ASN SER SEQRES 23 C 292 HIS HIS HIS HIS HIS HIS MODRES 4DKD ASN C 73 ASN GLYCOSYLATION SITE MODRES 4DKD ASN A 76 ASN GLYCOSYLATION SITE MODRES 4DKD ASN C 240 ASN GLYCOSYLATION SITE MODRES 4DKD ASN C 153 ASN GLYCOSYLATION SITE MODRES 4DKD ASN B 76 ASN GLYCOSYLATION SITE MODRES 4DKD ASN C 275 ASN GLYCOSYLATION SITE HET NAG D 1 14 HET NAG D 2 14 HET NAG E 1 14 HET NAG E 2 14 HET BMA A 303 11 HET BMA B 303 11 HET NAG C 401 14 HET NAG C 402 14 HET NAG C 403 14 HET NAG C 404 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM BMA BETA-D-MANNOPYRANOSE FORMUL 4 NAG 8(C8 H15 N O6) FORMUL 6 BMA 2(C6 H12 O6) FORMUL 12 HOH *16(H2 O) HELIX 1 1 ASN A 32 LEU A 45 1 14 HELIX 2 2 GLN A 46 LYS A 55 1 10 HELIX 3 3 PRO A 67 VAL A 71 5 5 HELIX 4 4 ARG A 73 ALA A 83 1 11 HELIX 5 5 SER A 86 ASP A 107 1 22 HELIX 6 6 SER A 115 GLY A 132 1 18 HELIX 7 7 SER A 139 ALA A 151 1 13 HELIX 8 8 ARG A 160 GLN A 182 1 23 HELIX 9 9 VAL A 185 GLN A 189 5 5 HELIX 10 10 GLU B 34 LEU B 45 1 12 HELIX 11 11 GLN B 46 LYS B 55 1 10 HELIX 12 12 PRO B 67 VAL B 71 5 5 HELIX 13 13 ARG B 73 ALA B 83 1 11 HELIX 14 14 GLU B 87 ASP B 107 1 21 HELIX 15 15 HIS B 113 GLN B 131 1 19 HELIX 16 16 GLY B 132 THR B 134 5 3 HELIX 17 17 SER B 139 ALA B 151 1 13 HELIX 18 18 ARG B 160 LYS B 181 1 22 HELIX 19 19 THR C 75 THR C 79 5 5 HELIX 20 20 ASP C 131 ALA C 136 5 6 HELIX 21 21 ARG C 144 ARG C 146 5 3 HELIX 22 22 LYS C 168 SER C 172 5 5 SHEET 1 A 2 ILE A 64 VAL A 66 0 SHEET 2 A 2 LYS A 157 VAL A 159 -1 O VAL A 159 N ILE A 64 SHEET 1 B 2 ILE B 64 SER B 65 0 SHEET 2 B 2 LEU B 158 VAL B 159 -1 O VAL B 159 N ILE B 64 SHEET 1 C 4 VAL C 22 GLU C 24 0 SHEET 2 C 4 VAL C 38 VAL C 43 -1 O ARG C 41 N GLU C 24 SHEET 3 C 4 SER C 66 THR C 71 -1 O SER C 67 N CYS C 42 SHEET 4 C 4 THR C 59 LEU C 60 -1 N THR C 59 O SER C 70 SHEET 1 D 2 VAL C 31 VAL C 32 0 SHEET 2 D 2 TYR C 100 VAL C 101 1 O TYR C 100 N VAL C 32 SHEET 1 E 2 TYR C 82 CYS C 84 0 SHEET 2 E 2 ALA C 95 ILE C 97 -1 O ILE C 97 N TYR C 82 SHEET 1 F 2 TRP C 108 VAL C 110 0 SHEET 2 F 2 CYS C 127 LEU C 129 -1 O LEU C 128 N ASN C 109 SHEET 1 G 4 GLU C 114 PHE C 118 0 SHEET 2 G 4 ILE C 191 GLN C 196 1 O GLN C 196 N VAL C 117 SHEET 3 G 4 ASP C 174 ALA C 179 -1 N TYR C 175 O ILE C 191 SHEET 4 G 4 VAL C 138 ARG C 142 -1 N SER C 139 O SER C 178 SHEET 1 H 4 GLU C 114 PHE C 118 0 SHEET 2 H 4 ILE C 191 GLN C 196 1 O GLN C 196 N VAL C 117 SHEET 3 H 4 ASP C 174 ALA C 179 -1 N TYR C 175 O ILE C 191 SHEET 4 H 4 VAL C 186 MET C 187 -1 O VAL C 186 N ALA C 179 SHEET 1 I 3 ALA C 123 LEU C 124 0 SHEET 2 I 3 THR C 163 ILE C 164 -1 O ILE C 164 N ALA C 123 SHEET 3 I 3 TYR C 154 SER C 155 -1 N SER C 155 O THR C 163 SHEET 1 J 4 ALA C 204 VAL C 208 0 SHEET 2 J 4 ALA C 220 SER C 228 -1 O VAL C 223 N VAL C 208 SHEET 3 J 4 ARG C 256 LEU C 265 -1 O LEU C 261 N CYS C 224 SHEET 4 J 4 GLN C 249 HIS C 253 -1 N ASP C 251 O GLN C 258 SHEET 1 K 3 ASP C 234 PHE C 236 0 SHEET 2 K 3 GLY C 274 SER C 281 -1 O SER C 281 N ASP C 234 SHEET 3 K 3 LYS C 286 PHE C 293 -1 O THR C 289 N CYS C 278 SSBOND 1 CYS A 35 CYS A 180 1555 1555 2.04 SSBOND 2 CYS A 177 CYS A 191 1555 1555 2.05 SSBOND 3 CYS B 35 CYS B 180 1555 1555 2.03 SSBOND 4 CYS B 177 CYS B 191 1555 1555 2.04 SSBOND 5 CYS C 42 CYS C 84 1555 1555 2.96 SSBOND 6 CYS C 127 CYS C 177 1555 1555 2.01 SSBOND 7 CYS C 224 CYS C 278 1555 1555 2.02 LINK ND2 ASN A 76 C1 NAG D 1 1555 1555 1.43 LINK ND2 ASN B 76 C1 NAG E 1 1555 1555 1.44 LINK ND2 ASN C 73 C1 NAG C 401 1555 1555 1.43 LINK ND2 ASN C 153 C1 NAG C 402 1555 1555 1.44 LINK ND2 ASN C 240 C1 NAG C 403 1555 1555 1.44 LINK ND2 ASN C 275 C1 NAG C 404 1555 1555 1.45 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.44 LINK O4 NAG E 1 C1 NAG E 2 1555 1555 1.44 CISPEP 1 GLU C 24 PRO C 25 0 -0.72 CISPEP 2 PRO C 54 SER C 55 0 12.35 CISPEP 3 SER C 55 PRO C 56 0 -7.26 CISPEP 4 VAL C 208 PRO C 209 0 2.12 CRYST1 101.361 101.361 175.252 90.00 90.00 120.00 P 31 2 1 12 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 0.009866 0.005696 0.000000 0.00000 SCALE2 0.000000 0.011392 0.000000 0.00000 SCALE3 0.000000 0.000000 0.005706 0.00000