HEADER IMMUNE SYSTEM 09-AUG-04 1U9K TITLE CRYSTAL STRUCTURE OF MOUSE TRIGGERING RECEPTOR EXPRESSED ON MYELOID TITLE 2 CELLS 1 (TREM-1) AT 1.76 COMPND MOL_ID: 1; COMPND 2 MOLECULE: TRIGGERING RECEPTOR EXPRESSED ON MYELOID CELLS 1; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: TRIGGERING RECEPTOR EXPRESSED IN MONOCYTES 1, TREM-1; COMPND 5 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 GENE: TREM; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21-(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET22B(+) KEYWDS ACTIVATING RECEPTORS, TREM-1, INNATE IMMUNITY, IMMUNE SYSTEM KEYWDS 2 RECEPTOR, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR M.S.KELKER,E.W.DEBLER,I.A.WILSON REVDAT 4 23-AUG-23 1U9K 1 REMARK LINK REVDAT 3 13-JUL-11 1U9K 1 VERSN REVDAT 2 24-FEB-09 1U9K 1 VERSN REVDAT 1 14-DEC-04 1U9K 0 JRNL AUTH M.S.KELKER,E.W.DEBLER,I.A.WILSON JRNL TITL CRYSTAL STRUCTURE OF MOUSE TRIGGERING RECEPTOR EXPRESSED ON JRNL TITL 2 MYELOID CELLS 1 (TREM-1) AT 1.76A JRNL REF J.MOL.BIOL. V. 344 1175 2004 JRNL REFN ISSN 0022-2836 JRNL PMID 15561137 JRNL DOI 10.1016/J.JMB.2004.10.009 REMARK 2 REMARK 2 RESOLUTION. 1.76 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.1.24 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) : 1.76 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 31.47 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 3 NUMBER OF REFLECTIONS : 26009 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) : 0.226 REMARK 3 R VALUE (WORKING SET) : 0.225 REMARK 3 FREE R VALUE : 0.248 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.900 REMARK 3 FREE R VALUE TEST SET COUNT : 1346 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) : 1.76 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.81 REMARK 3 REFLECTION IN BIN (WORKING SET) : 1446 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 BIN R VALUE (WORKING SET) : 0.3780 REMARK 3 BIN FREE R VALUE SET COUNT : 87 REMARK 3 BIN FREE R VALUE : 0.3650 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1784 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 3 REMARK 3 SOLVENT ATOMS : 59 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 22.45 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.10000 REMARK 3 B22 (A**2) : -0.02000 REMARK 3 B33 (A**2) : 0.12000 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 OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.130 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.122 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.105 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 3.553 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.950 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.942 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1837 ; 0.020 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 1667 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2501 ; 1.675 ; 1.967 REMARK 3 BOND ANGLES OTHERS (DEGREES): 3900 ; 0.814 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 218 ; 6.990 ; 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): 282 ; 0.100 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1990 ; 0.009 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 344 ; 0.011 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 281 ; 0.212 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 1884 ; 0.247 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION OTHERS (A): 1198 ; 0.088 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 39 ; 0.123 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): 5 ; 0.151 ; 0.200 REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 19 ; 0.304 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 20 ; 0.101 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 4 ; 0.543 ; 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): 1115 ; 0.926 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1836 ; 1.730 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 722 ; 3.011 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 665 ; 4.881 ; 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 : 2 REMARK 3 REMARK 3 TLS GROUP : 1 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : A 25 A 134 REMARK 3 ORIGIN FOR THE GROUP (A): -11.7060 -8.7410 30.5420 REMARK 3 T TENSOR REMARK 3 T11: 0.1005 T22: 0.0148 REMARK 3 T33: 0.0830 T12: -0.0036 REMARK 3 T13: 0.0092 T23: -0.0350 REMARK 3 L TENSOR REMARK 3 L11: 2.5456 L22: 4.1314 REMARK 3 L33: 1.8255 L12: -1.2114 REMARK 3 L13: 0.4388 L23: -2.2500 REMARK 3 S TENSOR REMARK 3 S11: 0.0378 S12: 0.0150 S13: 0.0231 REMARK 3 S21: -0.0090 S22: -0.0067 S23: 0.1066 REMARK 3 S31: -0.0444 S32: 0.0245 S33: -0.0312 REMARK 3 REMARK 3 TLS GROUP : 2 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : B 25 B 134 REMARK 3 ORIGIN FOR THE GROUP (A): 0.0430 -0.4310 0.5640 REMARK 3 T TENSOR REMARK 3 T11: 0.2389 T22: 0.3246 REMARK 3 T33: 0.1044 T12: 0.0234 REMARK 3 T13: 0.0251 T23: 0.1168 REMARK 3 L TENSOR REMARK 3 L11: 4.2104 L22: 2.3280 REMARK 3 L33: 3.8556 L12: -1.2487 REMARK 3 L13: -2.6164 L23: 1.2298 REMARK 3 S TENSOR REMARK 3 S11: 0.1847 S12: 0.4404 S13: 0.6059 REMARK 3 S21: -0.1301 S22: 0.0955 S23: -0.0421 REMARK 3 S31: -0.1746 S32: -0.2376 S33: -0.2802 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 1U9K COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 24-AUG-04. REMARK 100 THE DEPOSITION ID IS D_1000023414. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 25-JUN-04 REMARK 200 TEMPERATURE (KELVIN) : 93 REMARK 200 PH : 6.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL11-1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.97954 REMARK 200 MONOCHROMATOR : BENT MONOCHROMATOR (HORIZONTAL REMARK 200 FOCUSING) REMARK 200 OPTICS : FLAT MIRROR (VERTICAL FOCUSING), REMARK 200 SINGLE CRYSTAL SI(111) BENT REMARK 200 MONOCHROMATOR (HORIZONTAL REMARK 200 FOCUSING) 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 : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29567 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.760 REMARK 200 RESOLUTION RANGE LOW (A) : 31.470 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.3 REMARK 200 DATA REDUNDANCY : 6.300 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.12900 REMARK 200 FOR THE DATA SET : 39.8000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.76 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.79 REMARK 200 COMPLETENESS FOR SHELL (%) : 87.2 REMARK 200 DATA REDUNDANCY IN SHELL : 3.60 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.59500 REMARK 200 FOR SHELL : 2.500 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: PDB ENTRY 1SMO REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 57.70 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.90 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: MES, PEG 8000, ZINC ACETATE, PH 6.0, REMARK 280 VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277K 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 23.91850 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 62.60400 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.54050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 62.60400 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.91850 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.54050 REMARK 290 SMTRY3 4 0.000000 0.000000 -1.000000 0.00000 REMARK 290 REMARK 290 REMARK: NULL REMARK 300 REMARK 300 BIOMOLECULE: 1, 2 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 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 REMARK 350 BIOMOLECULE: 2 REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: MONOMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: 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 21 REMARK 465 ILE A 22 REMARK 465 VAL A 23 REMARK 465 LEU A 24 REMARK 465 ALA B 21 REMARK 465 ILE B 22 REMARK 465 VAL B 23 REMARK 465 LEU B 24 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 67 CE MET B 82 1.57 REMARK 500 CG MET A 46 O HOH A 158 2.07 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: CLOSE CONTACTS REMARK 500 REMARK 500 THE FOLLOWING ATOMS THAT ARE RELATED BY CRYSTALLOGRAPHIC REMARK 500 SYMMETRY ARE IN CLOSE CONTACT. AN ATOM LOCATED WITHIN 0.15 REMARK 500 ANGSTROMS OF A SYMMETRY RELATED ATOM IS ASSUMED TO BE ON A REMARK 500 SPECIAL POSITION AND IS, THEREFORE, LISTED IN REMARK 375 REMARK 500 INSTEAD OF REMARK 500. ATOMS WITH NON-BLANK ALTERNATE REMARK 500 LOCATION INDICATORS ARE NOT INCLUDED IN THE CALCULATIONS. REMARK 500 REMARK 500 DISTANCE CUTOFF: REMARK 500 2.2 ANGSTROMS FOR CONTACTS NOT INVOLVING HYDROGEN ATOMS REMARK 500 1.6 ANGSTROMS FOR CONTACTS INVOLVING HYDROGEN ATOMS REMARK 500 REMARK 500 ATM1 RES C SSEQI ATM2 RES C SSEQI SSYMOP DISTANCE REMARK 500 NE2 HIS A 81 O HOH A 173 3555 2.12 REMARK 500 O ASP A 30 OE1 GLU A 79 3545 2.19 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 ASP B 107 CB - CG - OD2 ANGL. DEV. = 6.0 DEGREES REMARK 500 PRO B 118 C - N - CA ANGL. DEV. = -9.2 DEGREES REMARK 500 PRO B 118 N - CA - C ANGL. DEV. = 31.5 DEGREES REMARK 500 PRO B 119 C - N - CD ANGL. DEV. = -41.7 DEGREES REMARK 500 PRO B 119 CB - CA - C ANGL. DEV. = 27.2 DEGREES REMARK 500 PRO B 119 N - CA - C ANGL. DEV. = -16.7 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 HIS A 117 64.22 -153.40 REMARK 500 PHE A 126 -131.42 60.52 REMARK 500 ASN B 50 54.16 -106.01 REMARK 500 HIS B 117 89.86 -166.78 REMARK 500 PHE B 126 -124.54 60.26 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: NON-CIS, NON-TRANS REMARK 500 REMARK 500 THE FOLLOWING PEPTIDE BONDS DEVIATE SIGNIFICANTLY FROM BOTH REMARK 500 CIS AND TRANS CONFORMATION. CIS BONDS, IF ANY, ARE LISTED REMARK 500 ON CISPEP RECORDS. TRANS IS DEFINED AS 180 +/- 30 AND REMARK 500 CIS IS DEFINED AS 0 +/- 30 DEGREES. REMARK 500 MODEL OMEGA REMARK 500 PRO B 118 PRO B 119 132.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: MAIN CHAIN PLANARITY REMARK 500 REMARK 500 THE FOLLOWING RESIDUES HAVE A PSEUDO PLANARITY REMARK 500 TORSION ANGLE, C(I) - CA(I) - N(I+1) - O(I), GREATER REMARK 500 10.0 DEGREES. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 500 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 500 I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI ANGLE REMARK 500 HIS B 117 -10.88 REMARK 500 REMARK 500 REMARK: NULL 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 ZN A 135 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 33 OE2 REMARK 620 2 ASP A 90 OD2 130.5 REMARK 620 3 GLU A 93 OE2 90.7 116.3 REMARK 620 4 THR A 134 OXT 117.9 104.7 87.6 REMARK 620 5 THR A 134 O 95.0 89.6 139.4 54.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 136 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 ASP A 60 OD2 REMARK 620 2 ASP A 60 OD1 51.6 REMARK 620 3 HIS A 117 ND1 91.4 102.0 REMARK 620 N 1 2 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN B 135 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU B 33 OE2 REMARK 620 2 ASP B 90 OD2 133.0 REMARK 620 3 GLU B 93 OE2 115.9 94.2 REMARK 620 4 THR B 134 OXT 105.7 107.3 94.2 REMARK 620 N 1 2 3 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 135 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN B 135 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 136 DBREF 1U9K A 21 134 UNP Q9JKE2 Q9JKE2_MOUSE 21 134 DBREF 1U9K B 21 134 UNP Q9JKE2 Q9JKE2_MOUSE 21 134 SEQRES 1 A 114 ALA ILE VAL LEU GLU GLU GLU ARG TYR ASP LEU VAL GLU SEQRES 2 A 114 GLY GLN THR LEU THR VAL LYS CYS PRO PHE ASN ILE MET SEQRES 3 A 114 LYS TYR ALA ASN SER GLN LYS ALA TRP GLN ARG LEU PRO SEQRES 4 A 114 ASP GLY LYS GLU PRO LEU THR LEU VAL VAL THR GLN ARG SEQRES 5 A 114 PRO PHE THR ARG PRO SER GLU VAL HIS MET GLY LYS PHE SEQRES 6 A 114 THR LEU LYS HIS ASP PRO SER GLU ALA MET LEU GLN VAL SEQRES 7 A 114 GLN MET THR ASP LEU GLN VAL THR ASP SER GLY LEU TYR SEQRES 8 A 114 ARG CYS VAL ILE TYR HIS PRO PRO ASN ASP PRO VAL VAL SEQRES 9 A 114 LEU PHE HIS PRO VAL ARG LEU VAL VAL THR SEQRES 1 B 114 ALA ILE VAL LEU GLU GLU GLU ARG TYR ASP LEU VAL GLU SEQRES 2 B 114 GLY GLN THR LEU THR VAL LYS CYS PRO PHE ASN ILE MET SEQRES 3 B 114 LYS TYR ALA ASN SER GLN LYS ALA TRP GLN ARG LEU PRO SEQRES 4 B 114 ASP GLY LYS GLU PRO LEU THR LEU VAL VAL THR GLN ARG SEQRES 5 B 114 PRO PHE THR ARG PRO SER GLU VAL HIS MET GLY LYS PHE SEQRES 6 B 114 THR LEU LYS HIS ASP PRO SER GLU ALA MET LEU GLN VAL SEQRES 7 B 114 GLN MET THR ASP LEU GLN VAL THR ASP SER GLY LEU TYR SEQRES 8 B 114 ARG CYS VAL ILE TYR HIS PRO PRO ASN ASP PRO VAL VAL SEQRES 9 B 114 LEU PHE HIS PRO VAL ARG LEU VAL VAL THR HET ZN A 135 1 HET ZN A 136 1 HET ZN B 135 1 HETNAM ZN ZINC ION FORMUL 3 ZN 3(ZN 2+) FORMUL 6 HOH *59(H2 O) HELIX 1 1 ASN A 44 ALA A 49 1 6 HELIX 2 2 PRO A 91 GLU A 93 5 3 HELIX 3 3 GLN A 104 SER A 108 5 5 HELIX 4 4 ASN B 44 ALA B 49 1 6 HELIX 5 5 PRO B 91 GLU B 93 5 3 HELIX 6 6 GLN B 104 SER B 108 5 5 SHEET 1 A 5 GLU A 27 VAL A 32 0 SHEET 2 A 5 VAL A 129 THR A 134 1 O ARG A 130 N TYR A 29 SHEET 3 A 5 GLY A 109 TYR A 116 -1 N GLY A 109 O LEU A 131 SHEET 4 A 5 GLN A 52 ARG A 57 -1 N GLN A 56 O ARG A 112 SHEET 5 A 5 LEU A 65 VAL A 69 -1 O LEU A 65 N ARG A 57 SHEET 1 B 4 GLU A 27 VAL A 32 0 SHEET 2 B 4 VAL A 129 THR A 134 1 O ARG A 130 N TYR A 29 SHEET 3 B 4 GLY A 109 TYR A 116 -1 N GLY A 109 O LEU A 131 SHEET 4 B 4 VAL A 123 VAL A 124 -1 O VAL A 123 N ILE A 115 SHEET 1 C 4 LEU A 37 PRO A 42 0 SHEET 2 C 4 MET A 95 MET A 100 -1 O LEU A 96 N CYS A 41 SHEET 3 C 4 PHE A 85 ASP A 90 -1 N LYS A 88 O GLN A 97 SHEET 4 C 4 SER A 78 MET A 82 -1 N SER A 78 O HIS A 89 SHEET 1 D 5 GLU B 27 VAL B 32 0 SHEET 2 D 5 VAL B 129 THR B 134 1 O ARG B 130 N GLU B 27 SHEET 3 D 5 GLY B 109 TYR B 116 -1 N GLY B 109 O LEU B 131 SHEET 4 D 5 GLN B 52 ARG B 57 -1 N GLN B 56 O ARG B 112 SHEET 5 D 5 LEU B 65 VAL B 69 -1 O LEU B 65 N ARG B 57 SHEET 1 E 4 GLU B 27 VAL B 32 0 SHEET 2 E 4 VAL B 129 THR B 134 1 O ARG B 130 N GLU B 27 SHEET 3 E 4 GLY B 109 TYR B 116 -1 N GLY B 109 O LEU B 131 SHEET 4 E 4 VAL B 123 VAL B 124 -1 O VAL B 123 N ILE B 115 SHEET 1 F 4 LEU B 37 PRO B 42 0 SHEET 2 F 4 MET B 95 MET B 100 -1 O LEU B 96 N CYS B 41 SHEET 3 F 4 PHE B 85 ASP B 90 -1 N LYS B 88 O GLN B 97 SHEET 4 F 4 SER B 78 MET B 82 -1 N SER B 78 O HIS B 89 SSBOND 1 CYS A 41 CYS A 113 1555 1555 2.09 SSBOND 2 CYS B 41 CYS B 113 1555 1555 2.09 LINK OE2 GLU A 33 ZN ZN A 135 1555 1555 1.84 LINK OD2 ASP A 60 ZN ZN A 136 3455 1555 2.63 LINK OD1 ASP A 60 ZN ZN A 136 3455 1555 2.31 LINK OD2 ASP A 90 ZN ZN A 135 3545 1555 1.99 LINK OE2 GLU A 93 ZN ZN A 135 3545 1555 2.20 LINK ND1 HIS A 117 ZN ZN A 136 1555 1555 2.28 LINK OXT THR A 134 ZN ZN A 135 1555 1555 1.97 LINK O THR A 134 ZN ZN A 135 1555 1555 2.73 LINK OE2 GLU B 33 ZN ZN B 135 1555 1555 1.82 LINK OD2 ASP B 90 ZN ZN B 135 4545 1555 1.89 LINK OE2 GLU B 93 ZN ZN B 135 4545 1555 2.02 LINK OXT THR B 134 ZN ZN B 135 1555 1555 1.83 CISPEP 1 ARG A 72 PRO A 73 0 -3.53 CISPEP 2 PRO A 118 PRO A 119 0 3.12 CISPEP 3 ARG B 72 PRO B 73 0 -9.02 SITE 1 AC1 4 GLU A 33 ASP A 90 GLU A 93 THR A 134 SITE 1 AC2 4 GLU B 33 ASP B 90 GLU B 93 THR B 134 SITE 1 AC3 2 ASP A 60 HIS A 117 CRYST1 47.837 49.081 125.208 90.00 90.00 90.00 P 21 21 21 8 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 0.020904 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020374 0.000000 0.00000 SCALE3 0.000000 0.000000 0.007987 0.00000