PDB Short entry for 3BIB HEADER IMMUNE SYSTEM 30-NOV-07 3BIB TITLE TIM-4 IN COMPLEX WITH PHOSPHATIDYLSERINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: T-CELL IMMUNOGLOBULIN AND MUCIN DOMAIN-CONTAINING PROTEIN COMPND 3 4; COMPND 4 CHAIN: X; COMPND 5 FRAGMENT: N-TERMINAL CYS-RICH DOMAIN; COMPND 6 SYNONYM: TIMD-4, T-CELL MEMBRANE PROTEIN 4, TIM-4, SPLEEN, MUCIN- COMPND 7 CONTAINING, KNOCKOUT OF LYMPHOTOXIN PROTEIN, SMUCKLER; COMPND 8 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: HOUSE MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 STRAIN: KNOWLES SOLTER, C57BL/6J; SOURCE 6 GENE: TIMD4, TIM4; SOURCE 7 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21; SOURCE 8 EXPRESSION_SYSTEM_TAXID: 511693; SOURCE 9 EXPRESSION_SYSTEM_STRAIN: BL21; SOURCE 10 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 11 EXPRESSION_SYSTEM_PLASMID: PET27B(+) KEYWDS BETA BARREL, IMMUNOGLOBULIN FOLD, IGV DOMAIN, TIM, GLYCOPROTEIN, KEYWDS 2 IMMUNOGLOBULIN DOMAIN, MEMBRANE, POLYMORPHISM, TRANSMEMBRANE, IMMUNE KEYWDS 3 SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR C.SANTIAGO,A.BALLESTEROS,G.G.KAPLAN,G.J.FREEMAN,J.M.CASASNOVAS REVDAT 3 03-APR-24 3BIB 1 REMARK SEQADV REVDAT 2 24-FEB-09 3BIB 1 VERSN REVDAT 1 01-JAN-08 3BIB 0 JRNL AUTH C.SANTIAGO,A.BALLESTEROS,L.MARTINEZ-MUNOZ,M.MELLADO, JRNL AUTH 2 G.G.KAPLAN,G.J.FREEMAN,J.M.CASASNOVAS JRNL TITL STRUCTURES OF T CELL IMMUNOGLOBULIN MUCIN PROTEIN 4 SHOW A JRNL TITL 2 METAL-ION-DEPENDENT LIGAND BINDING SITE WHERE JRNL TITL 3 PHOSPHATIDYLSERINE BINDS. JRNL REF IMMUNITY V. 27 941 2007 JRNL REFN ISSN 1074-7613 JRNL PMID 18083575 JRNL DOI 10.1016/J.IMMUNI.2007.11.008 REMARK 2 REMARK 2 RESOLUTION. 2.50 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 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) : 2.50 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 15.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 3 NUMBER OF REFLECTIONS : 6421 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) : 0.221 REMARK 3 R VALUE (WORKING SET) : 0.219 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.800 REMARK 3 FREE R VALUE TEST SET COUNT : 321 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) : 2.50 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.56 REMARK 3 REFLECTION IN BIN (WORKING SET) : 450 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.0 REMARK 3 BIN R VALUE (WORKING SET) : 0.2240 REMARK 3 BIN FREE R VALUE SET COUNT : 23 REMARK 3 BIN FREE R VALUE : 0.2730 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 855 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 27 REMARK 3 SOLVENT ATOMS : 47 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 36.02 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 1.34000 REMARK 3 B22 (A**2) : 1.34000 REMARK 3 B33 (A**2) : -2.01000 REMARK 3 B12 (A**2) : 0.67000 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): NULL REMARK 3 ESU BASED ON FREE R VALUE (A): 0.240 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.169 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 16.357 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.928 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.909 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 899 ; 0.008 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1213 ; 1.114 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 108 ; 6.214 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 37 ;32.398 ;22.432 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 157 ;14.926 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 9 ;18.573 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 132 ; 0.074 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 658 ; 0.003 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 338 ; 0.189 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 598 ; 0.298 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 46 ; 0.110 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 2 ; 0.148 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 23 ; 0.165 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 5 ; 0.111 ; 0.200 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): 543 ; 0.640 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 876 ; 1.115 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 374 ; 5.219 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 337 ; 4.125 ; 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): 917 ; 6.153 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 48 ; 2.580 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 881 ; 2.283 ; 3.000 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 : 1.20 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 3BIB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 10-DEC-07. REMARK 100 THE DEPOSITION ID IS D_1000045556. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-NOV-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 5.6 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) : 0.97925 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ADSC QUANTUM 315 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : XDS REMARK 200 DATA SCALING SOFTWARE : SCALA REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 6799 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 25.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.9 REMARK 200 DATA REDUNDANCY : 11.00 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : 5.70000 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 9.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.64 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 10.20 REMARK 200 R MERGE FOR SHELL (I) : 0.16800 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : 4.400 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: TIM-2 HOMOLOGOUS MODEL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 63.63 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.38 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.1 M SODIUM CITRATE, 10 % JEFFAMINE, REMARK 280 10 MM FECL3. PROTEIN PRE-INCUBATED WITH 5 MM 1,2 DICAPROYL-SN- REMARK 280 GLYCERO-3-(PHOSPHO-L-SERINE) AND 5 MM CACL2, PH 5.6, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 294K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 63 2 2 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z REMARK 290 3555 -X+Y,-X,Z REMARK 290 4555 -X,-Y,Z+1/2 REMARK 290 5555 Y,-X+Y,Z+1/2 REMARK 290 6555 X-Y,X,Z+1/2 REMARK 290 7555 Y,X,-Z REMARK 290 8555 X-Y,-Y,-Z REMARK 290 9555 -X,-X+Y,-Z REMARK 290 10555 -Y,-X,-Z+1/2 REMARK 290 11555 -X+Y,Y,-Z+1/2 REMARK 290 12555 X,X-Y,-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 -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 0.00000 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 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 69.69500 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 69.69500 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 69.69500 REMARK 290 SMTRY1 7 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 7 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 9 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 9 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 9 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 10 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 10 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 10 0.000000 0.000000 -1.000000 69.69500 REMARK 290 SMTRY1 11 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 11 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 11 0.000000 0.000000 -1.000000 69.69500 REMARK 290 SMTRY1 12 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 12 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 12 0.000000 0.000000 -1.000000 69.69500 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: X 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 375 REMARK 375 SPECIAL POSITION REMARK 375 THE FOLLOWING ATOMS ARE FOUND TO BE WITHIN 0.15 ANGSTROMS REMARK 375 OF A SYMMETRY RELATED ATOM AND ARE ASSUMED TO BE ON SPECIAL REMARK 375 POSITIONS. REMARK 375 REMARK 375 ATOM RES CSSEQI REMARK 375 HOH X 145 LIES ON A SPECIAL POSITION. 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 MET X 1 REMARK 465 SER X 2 REMARK 465 GLU X 3 REMARK 465 LEU X 113 REMARK 465 VAL X 114 REMARK 465 PRO X 115 REMARK 465 ARG X 116 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 X 22 37.25 -92.00 REMARK 500 LYS X 41 -160.35 59.73 REMARK 500 LEU X 47 141.04 -174.56 REMARK 500 ASP X 50 -138.94 -98.31 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 PSF X 118 REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 NA X 117 NA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 VAL X 94 O REMARK 620 2 GLY X 96 O 90.5 REMARK 620 3 ASN X 99 OD1 84.7 84.8 REMARK 620 4 ASP X 100 OD1 83.5 167.0 106.0 REMARK 620 5 PSF X 118 O4 172.3 95.2 101.0 89.9 REMARK 620 6 HOH X 165 O 67.7 98.9 152.1 68.1 106.2 REMARK 620 N 1 2 3 4 5 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE NA X 117 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE PSF X 118 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2OR8 RELATED DB: PDB REMARK 900 TIM-1 REMARK 900 RELATED ID: 2OR7 RELATED DB: PDB REMARK 900 TIM-2 REMARK 900 RELATED ID: 2OYP RELATED DB: PDB REMARK 900 TIM-3 REMARK 900 RELATED ID: 3BI9 RELATED DB: PDB REMARK 900 RELATED ID: 3BIA RELATED DB: PDB DBREF 3BIB X 2 112 UNP Q6U7R4 TIMD4_MOUSE 24 134 SEQADV 3BIB MET X 1 UNP Q6U7R4 INITIATING METHIONINE SEQADV 3BIB LEU X 113 UNP Q6U7R4 EXPRESSION TAG SEQADV 3BIB VAL X 114 UNP Q6U7R4 EXPRESSION TAG SEQADV 3BIB PRO X 115 UNP Q6U7R4 EXPRESSION TAG SEQADV 3BIB ARG X 116 UNP Q6U7R4 EXPRESSION TAG SEQRES 1 X 116 MET SER GLU ASP THR ILE ILE GLY PHE LEU GLY GLN PRO SEQRES 2 X 116 VAL THR LEU PRO CYS HIS TYR LEU SER TRP SER GLN SER SEQRES 3 X 116 ARG ASN SER MET CYS TRP GLY LYS GLY SER CYS PRO ASN SEQRES 4 X 116 SER LYS CYS ASN ALA GLU LEU LEU ARG THR ASP GLY THR SEQRES 5 X 116 ARG ILE ILE SER ARG LYS SER THR LYS TYR THR LEU LEU SEQRES 6 X 116 GLY LYS VAL GLN PHE GLY GLU VAL SER LEU THR ILE SER SEQRES 7 X 116 ASN THR ASN ARG GLY ASP SER GLY VAL TYR CYS CYS ARG SEQRES 8 X 116 ILE GLU VAL PRO GLY TRP PHE ASN ASP VAL LYS LYS ASN SEQRES 9 X 116 VAL ARG LEU GLU LEU ARG ARG ALA LEU VAL PRO ARG HET NA X 117 1 HET PSF X 118 26 HETNAM NA SODIUM ION HETNAM PSF 1,2-DICAPROYL-SN-PHOSPHATIDYL-L-SERINE HETSYN PSF PHOSPHATIDYLSERINE FORMUL 2 NA NA 1+ FORMUL 3 PSF C18 H34 N O10 P FORMUL 4 HOH *47(H2 O) HELIX 1 1 LYS X 67 GLY X 71 5 5 HELIX 2 2 ASN X 81 SER X 85 5 5 SHEET 1 A 6 THR X 5 PHE X 9 0 SHEET 2 A 6 VAL X 101 ARG X 110 1 O ARG X 106 N ILE X 6 SHEET 3 A 6 GLY X 86 GLU X 93 -1 N CYS X 90 O LYS X 103 SHEET 4 A 6 SER X 29 LYS X 34 -1 N SER X 29 O GLU X 93 SHEET 5 A 6 GLU X 45 THR X 49 -1 O LEU X 46 N TRP X 32 SHEET 6 A 6 ILE X 54 ARG X 57 -1 O SER X 56 N ARG X 48 SHEET 1 B 3 VAL X 14 LEU X 16 0 SHEET 2 B 3 LEU X 75 ILE X 77 -1 O LEU X 75 N LEU X 16 SHEET 3 B 3 TYR X 62 LEU X 64 -1 N THR X 63 O THR X 76 SSBOND 1 CYS X 18 CYS X 90 1555 1555 2.06 SSBOND 2 CYS X 31 CYS X 42 1555 1555 2.05 SSBOND 3 CYS X 37 CYS X 89 1555 1555 2.05 LINK O VAL X 94 NA NA X 117 1555 1555 2.44 LINK O GLY X 96 NA NA X 117 1555 1555 2.56 LINK OD1 ASN X 99 NA NA X 117 1555 1555 2.33 LINK OD1 ASP X 100 NA NA X 117 1555 1555 2.74 LINK NA NA X 117 O4 PSF X 118 1555 1555 2.22 LINK NA NA X 117 O HOH X 165 1555 1555 2.90 SITE 1 AC1 6 VAL X 94 GLY X 96 ASN X 99 ASP X 100 SITE 2 AC1 6 PSF X 118 HOH X 165 SITE 1 AC2 13 ASN X 39 SER X 40 LYS X 41 ARG X 91 SITE 2 AC2 13 GLU X 93 GLY X 96 TRP X 97 PHE X 98 SITE 3 AC2 13 ASN X 99 ASP X 100 NA X 117 HOH X 128 SITE 4 AC2 13 HOH X 165 CRYST1 66.260 66.260 139.390 90.00 90.00 120.00 P 63 2 2 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 0.015092 0.008713 0.000000 0.00000 SCALE2 0.000000 0.017427 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007174 0.00000