HEADER IMMUNE SYSTEM 15-AUG-06 2I25 TITLE CRYSTAL STRUCTURE ANALYSIS OF THE NURSE SHARK NEW ANTIGEN RECEPTOR TITLE 2 PBLA8 VARIABLE DOMAIN IN COMPLEX WITH LYSOZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: NEW ANTIGEN RECEPTOR PBLA8; COMPND 3 CHAIN: N, O; COMPND 4 FRAGMENT: VARIABLE DOMAIN; COMPND 5 ENGINEERED: YES; COMPND 6 MOL_ID: 2; COMPND 7 MOLECULE: LYSOZYME C; COMPND 8 CHAIN: L, M; COMPND 9 SYNONYM: 1,4-BETA-N-ACETYLMURAMIDASE C, ALLERGEN GAL D 4, GAL D IV; COMPND 10 EC: 3.2.1.17 SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GINGLYMOSTOMA CIRRATUM; SOURCE 3 ORGANISM_COMMON: NURSE SHARK; SOURCE 4 ORGANISM_TAXID: 7801; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: XL1-BLUE; SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PIMS100; SOURCE 10 MOL_ID: 2; SOURCE 11 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 12 ORGANISM_COMMON: CHICKEN; SOURCE 13 ORGANISM_TAXID: 9031 KEYWDS IMMUNOGLOBULIN FOLD, PROTEIN-PROTEIN COMPLEX, IMMUNE SYSTEM EXPDTA X-RAY DIFFRACTION AUTHOR R.L.STANFIELD,I.A.WILSON REVDAT 4 13-JUL-11 2I25 1 VERSN REVDAT 3 24-FEB-09 2I25 1 VERSN REVDAT 2 27-MAR-07 2I25 1 JRNL REVDAT 1 06-MAR-07 2I25 0 JRNL AUTH R.L.STANFIELD,H.DOOLEY,P.VERDINO,M.F.FLAJNIK,I.A.WILSON JRNL TITL MATURATION OF SHARK SINGLE-DOMAIN (IGNAR) ANTIBODIES: JRNL TITL 2 EVIDENCE FOR INDUCED-FIT BINDING JRNL REF J.MOL.BIOL. V. 367 358 2007 JRNL REFN ISSN 0022-2836 JRNL PMID 17258766 JRNL DOI 10.1016/J.JMB.2006.12.045 REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0019 REMARK 3 AUTHORS : MURSHUDOV,VAGIN,DODSON REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 33.71 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 57232 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) : 0.187 REMARK 3 R VALUE (WORKING SET) : 0.185 REMARK 3 FREE R VALUE : 0.211 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 3041 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) : 1.80 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.85 REMARK 3 REFLECTION IN BIN (WORKING SET) : 4270 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 100.00 REMARK 3 BIN R VALUE (WORKING SET) : 0.2220 REMARK 3 BIN FREE R VALUE SET COUNT : 238 REMARK 3 BIN FREE R VALUE : 0.2670 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 3784 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 317 REMARK 3 REMARK 3 B VALUES. REMARK 3 B VALUE TYPE : LIKELY RESIDUAL REMARK 3 FROM WILSON PLOT (A**2) : 28.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 31.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.63000 REMARK 3 B22 (A**2) : -0.69000 REMARK 3 B33 (A**2) : 0.07000 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): 0.108 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.103 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.071 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 4.378 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.958 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.948 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 3864 ; 0.021 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 2678 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5234 ; 1.762 ; 1.922 REMARK 3 BOND ANGLES OTHERS (DEGREES): 6396 ; 1.006 ; 3.008 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 485 ; 6.379 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 187 ;35.627 ;22.781 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 631 ;12.790 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 44 ;15.690 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 557 ; 0.110 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4397 ; 0.008 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 849 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 701 ; 0.215 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 2830 ; 0.216 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1885 ; 0.182 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 2159 ; 0.089 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 277 ; 0.145 ; 0.200 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): 8 ; 0.074 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 55 ; 0.244 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 18 ; 0.121 ; 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): 3085 ; 1.398 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1017 ; 0.364 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 3849 ; 1.687 ; 2.000 REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1735 ; 2.808 ; 3.000 REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1385 ; 3.922 ; 4.500 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 : 4 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 : N 2 N 115 REMARK 3 ORIGIN FOR THE GROUP (A): 38.1873 36.2836 85.9140 REMARK 3 T TENSOR REMARK 3 T11: -0.1009 T22: -0.1585 REMARK 3 T33: -0.1471 T12: 0.0107 REMARK 3 T13: 0.0216 T23: -0.0030 REMARK 3 L TENSOR REMARK 3 L11: 3.2609 L22: 2.8176 REMARK 3 L33: 1.7240 L12: 0.1888 REMARK 3 L13: -1.2084 L23: 0.2602 REMARK 3 S TENSOR REMARK 3 S11: -0.0422 S12: -0.1135 S13: 0.0922 REMARK 3 S21: 0.2710 S22: 0.1092 S23: 0.1695 REMARK 3 S31: 0.0248 S32: -0.0951 S33: -0.0670 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 : L 1 L 129 REMARK 3 ORIGIN FOR THE GROUP (A): 66.4622 44.1239 71.9154 REMARK 3 T TENSOR REMARK 3 T11: -0.1435 T22: 0.0109 REMARK 3 T33: 0.0565 T12: -0.0562 REMARK 3 T13: 0.0014 T23: -0.0741 REMARK 3 L TENSOR REMARK 3 L11: 2.7553 L22: 3.1454 REMARK 3 L33: 3.2292 L12: -0.1660 REMARK 3 L13: -1.5814 L23: 1.2420 REMARK 3 S TENSOR REMARK 3 S11: 0.1230 S12: -0.3612 S13: 0.4335 REMARK 3 S21: 0.1295 S22: 0.0974 S23: -0.4024 REMARK 3 S31: -0.1851 S32: 0.5693 S33: -0.2204 REMARK 3 REMARK 3 TLS GROUP : 3 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : O 2 O 118 REMARK 3 ORIGIN FOR THE GROUP (A): 42.5569 15.0887 80.3406 REMARK 3 T TENSOR REMARK 3 T11: -0.1477 T22: -0.1653 REMARK 3 T33: -0.1345 T12: 0.0006 REMARK 3 T13: -0.0122 T23: -0.0004 REMARK 3 L TENSOR REMARK 3 L11: 1.7450 L22: 1.7922 REMARK 3 L33: 5.8087 L12: -0.0193 REMARK 3 L13: 2.2874 L23: -0.7129 REMARK 3 S TENSOR REMARK 3 S11: 0.1098 S12: -0.1244 S13: -0.1964 REMARK 3 S21: 0.1138 S22: 0.0660 S23: -0.0811 REMARK 3 S31: 0.2100 S32: 0.0367 S33: -0.1758 REMARK 3 REMARK 3 TLS GROUP : 4 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : M 1 M 129 REMARK 3 ORIGIN FOR THE GROUP (A): 29.4558 24.0599 50.9128 REMARK 3 T TENSOR REMARK 3 T11: -0.1045 T22: -0.1123 REMARK 3 T33: -0.1636 T12: -0.0136 REMARK 3 T13: -0.0256 T23: 0.0225 REMARK 3 L TENSOR REMARK 3 L11: 2.5673 L22: 2.2580 REMARK 3 L33: 3.4379 L12: 1.1276 REMARK 3 L13: 1.7370 L23: 1.0383 REMARK 3 S TENSOR REMARK 3 S11: -0.2024 S12: 0.2608 S13: 0.1391 REMARK 3 S21: -0.3359 S22: 0.1204 S23: 0.1501 REMARK 3 S31: -0.5025 S32: 0.0137 S33: 0.0820 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 2I25 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 16-AUG-06. REMARK 100 THE RCSB ID CODE IS RCSB039041. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 07-MAY-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.3 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRL REMARK 200 BEAMLINE : BL9-2 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.95369 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 325 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 60320 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.800 REMARK 200 RESOLUTION RANGE LOW (A) : 33.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 200 DATA REDUNDANCY : 4.200 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.06400 REMARK 200 FOR THE DATA SET : 19.7000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.80 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.85 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 4.10 REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.53500 REMARK 200 FOR SHELL : 1.700 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: AMORE REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.40 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 38% PEG 400, 0.1M TRIS, PH 8.3, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 295K 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 36.98950 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 53.68150 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 41.35950 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 53.68150 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 36.98950 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 41.35950 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: N, L 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: DIMERIC REMARK 350 APPLY THE FOLLOWING TO CHAINS: O, M 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 N 1 REMARK 465 HIS N 116 REMARK 465 HIS N 117 REMARK 465 HIS N 118 REMARK 465 HIS N 119 REMARK 465 HIS N 120 REMARK 465 HIS N 121 REMARK 465 ALA O 1 REMARK 465 HIS O 119 REMARK 465 HIS O 120 REMARK 465 HIS O 121 REMARK 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 ALA N 115 O 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 SER N 43 CB SER N 43 OG -0.079 REMARK 500 GLU N 46 CB GLU N 46 CG -0.117 REMARK 500 ALA N 115 C ALA N 115 O 0.530 REMARK 500 GLU L 7 CD GLU L 7 OE2 0.111 REMARK 500 GLU O 46 CB GLU O 46 CG -0.307 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 ARG N 38 NE - CZ - NH1 ANGL. DEV. = 4.5 DEGREES REMARK 500 ARG N 38 NE - CZ - NH2 ANGL. DEV. = -4.3 DEGREES REMARK 500 ALA N 115 CA - C - O ANGL. DEV. = -28.0 DEGREES REMARK 500 ARG L 112 NE - CZ - NH2 ANGL. DEV. = -3.2 DEGREES REMARK 500 ARG O 25 NE - CZ - NH1 ANGL. DEV. = 3.5 DEGREES REMARK 500 GLU O 46 CG - CD - OE1 ANGL. DEV. = -14.0 DEGREES REMARK 500 GLU O 46 CG - CD - OE2 ANGL. DEV. = 12.9 DEGREES REMARK 500 ILE O 49 CB - CA - C ANGL. DEV. = -13.4 DEGREES REMARK 500 ARG M 5 NE - CZ - NH1 ANGL. DEV. = 3.1 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 ASP O 26 114.46 -161.89 REMARK 500 ARG M 128 52.38 -96.36 REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH N 196 DISTANCE = 5.18 ANGSTROMS REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2I24 RELATED DB: PDB REMARK 900 RELATED ID: 2I26 RELATED DB: PDB REMARK 900 RELATED ID: 2I27 RELATED DB: PDB REMARK 999 REMARK 999 SEQUENCE REMARK 999 AT THE TIME OF PROCESSING, A UNP REFERENCE SEQUENCE REMARK 999 WAS NOT AVAILABLE FOR THE NEW ANTIGEN RECEPTOR PBLA8. DBREF 2I25 N 1 112 UNP Q8AXH5 Q8AXH5_GINCI 1 112 DBREF 2I25 L 1 129 UNP P00698 LYSC_CHICK 19 147 DBREF 2I25 O 1 112 UNP Q8AXH5 Q8AXH5_GINCI 1 112 DBREF 2I25 M 1 129 UNP P00698 LYSC_CHICK 19 147 SEQRES 1 N 121 ALA ARG VAL ASP GLN THR PRO GLN ARG ILE THR LYS GLU SEQRES 2 N 121 THR GLY GLU SER LEU THR ILE ASN CYS VAL VAL ARG ASP SEQRES 3 N 121 SER ARG CYS VAL LEU SER THR GLY TYR TRP TYR ARG LYS SEQRES 4 N 121 PRO PRO GLY SER ARG ASN GLU GLU SER ILE SER ASP GLY SEQRES 5 N 121 GLY ARG TYR VAL GLU THR VAL ASN ARG GLY SER LYS SER SEQRES 6 N 121 PHE SER LEU ARG ILE ASN ASP LEU THR VAL LYS ASP SER SEQRES 7 N 121 GLY THR TYR ARG CYS LYS PRO GLU SER ARG TYR GLY SER SEQRES 8 N 121 TYR ASP ALA VAL CYS ALA ALA LEU ASN ASP GLN TYR GLY SEQRES 9 N 121 GLY GLY THR VAL VAL THR VAL ASN ALA ALA ALA HIS HIS SEQRES 10 N 121 HIS HIS HIS HIS SEQRES 1 L 129 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS SEQRES 2 L 129 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY SEQRES 3 L 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN SEQRES 4 L 129 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP SEQRES 5 L 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN SEQRES 6 L 129 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE SEQRES 7 L 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER SEQRES 8 L 129 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY SEQRES 9 L 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY SEQRES 10 L 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU SEQRES 1 O 121 ALA ARG VAL ASP GLN THR PRO GLN ARG ILE THR LYS GLU SEQRES 2 O 121 THR GLY GLU SER LEU THR ILE ASN CYS VAL VAL ARG ASP SEQRES 3 O 121 SER ARG CYS VAL LEU SER THR GLY TYR TRP TYR ARG LYS SEQRES 4 O 121 PRO PRO GLY SER ARG ASN GLU GLU SER ILE SER ASP GLY SEQRES 5 O 121 GLY ARG TYR VAL GLU THR VAL ASN ARG GLY SER LYS SER SEQRES 6 O 121 PHE SER LEU ARG ILE ASN ASP LEU THR VAL LYS ASP SER SEQRES 7 O 121 GLY THR TYR ARG CYS LYS PRO GLU SER ARG TYR GLY SER SEQRES 8 O 121 TYR ASP ALA VAL CYS ALA ALA LEU ASN ASP GLN TYR GLY SEQRES 9 O 121 GLY GLY THR VAL VAL THR VAL ASN ALA ALA ALA HIS HIS SEQRES 10 O 121 HIS HIS HIS HIS SEQRES 1 M 129 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS SEQRES 2 M 129 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY SEQRES 3 M 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN SEQRES 4 M 129 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP SEQRES 5 M 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN SEQRES 6 M 129 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE SEQRES 7 M 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER SEQRES 8 M 129 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY SEQRES 9 M 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY SEQRES 10 M 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU FORMUL 5 HOH *317(H2 O) HELIX 1 1 THR N 74 SER N 78 5 5 HELIX 2 2 ASP N 93 ASN N 100 1 8 HELIX 3 3 GLY L 4 HIS L 15 1 12 HELIX 4 4 ASN L 19 TYR L 23 5 5 HELIX 5 5 SER L 24 ASN L 37 1 14 HELIX 6 6 PRO L 79 SER L 85 5 7 HELIX 7 7 ILE L 88 SER L 100 1 13 HELIX 8 8 ASN L 103 ALA L 107 5 5 HELIX 9 9 TRP L 108 CYS L 115 1 8 HELIX 10 10 ASP L 119 ARG L 125 5 7 HELIX 11 11 THR O 74 SER O 78 5 5 HELIX 12 12 ASP O 93 ASN O 100 1 8 HELIX 13 13 GLY M 4 HIS M 15 1 12 HELIX 14 14 ASN M 19 TYR M 23 5 5 HELIX 15 15 SER M 24 ASN M 37 1 14 HELIX 16 16 PRO M 79 SER M 85 5 7 HELIX 17 17 ILE M 88 SER M 100 1 13 HELIX 18 18 ASN M 103 ALA M 107 5 5 HELIX 19 19 TRP M 108 CYS M 115 1 8 HELIX 20 20 ASP M 119 ARG M 125 5 7 SHEET 1 A 4 VAL N 3 THR N 6 0 SHEET 2 A 4 LEU N 18 VAL N 24 -1 O VAL N 23 N ASP N 4 SHEET 3 A 4 SER N 65 ILE N 70 -1 O PHE N 66 N CYS N 22 SHEET 4 A 4 TYR N 55 ASN N 60 -1 N ASN N 60 O SER N 65 SHEET 1 B 5 ARG N 9 GLU N 13 0 SHEET 2 B 5 THR N 107 ASN N 112 1 O ASN N 112 N LYS N 12 SHEET 3 B 5 GLY N 79 GLU N 86 -1 N GLY N 79 O VAL N 109 SHEET 4 B 5 THR N 33 LYS N 39 -1 N LYS N 39 O THR N 80 SHEET 5 B 5 GLU N 47 ILE N 49 -1 O GLU N 47 N ARG N 38 SHEET 1 C 3 THR L 43 ARG L 45 0 SHEET 2 C 3 THR L 51 TYR L 53 -1 O ASP L 52 N ASN L 44 SHEET 3 C 3 ILE L 58 ASN L 59 -1 O ILE L 58 N TYR L 53 SHEET 1 D 4 VAL O 3 THR O 6 0 SHEET 2 D 4 LEU O 18 VAL O 24 -1 O VAL O 23 N ASP O 4 SHEET 3 D 4 SER O 65 ILE O 70 -1 O ILE O 70 N LEU O 18 SHEET 4 D 4 TYR O 55 ASN O 60 -1 N ASN O 60 O SER O 65 SHEET 1 E 5 ARG O 9 GLU O 13 0 SHEET 2 E 5 THR O 107 ASN O 112 1 O ASN O 112 N LYS O 12 SHEET 3 E 5 GLY O 79 GLU O 86 -1 N GLY O 79 O VAL O 109 SHEET 4 E 5 THR O 33 LYS O 39 -1 N LYS O 39 O THR O 80 SHEET 5 E 5 GLU O 47 ILE O 49 -1 O GLU O 47 N ARG O 38 SHEET 1 F 3 THR M 43 ARG M 45 0 SHEET 2 F 3 THR M 51 TYR M 53 -1 O ASP M 52 N ASN M 44 SHEET 3 F 3 ILE M 58 ASN M 59 -1 O ILE M 58 N TYR M 53 SSBOND 1 CYS N 22 CYS N 83 1555 1555 1.98 SSBOND 2 CYS N 29 CYS N 96 1555 1555 2.18 SSBOND 3 CYS L 6 CYS L 127 1555 1555 2.10 SSBOND 4 CYS L 30 CYS L 115 1555 1555 2.20 SSBOND 5 CYS L 64 CYS L 80 1555 1555 2.04 SSBOND 6 CYS L 76 CYS L 94 1555 1555 2.10 SSBOND 7 CYS O 22 CYS O 83 1555 1555 1.98 SSBOND 8 CYS O 29 CYS O 96 1555 1555 2.06 SSBOND 9 CYS M 6 CYS M 127 1555 1555 2.09 SSBOND 10 CYS M 30 CYS M 115 1555 1555 2.23 SSBOND 11 CYS M 64 CYS M 80 1555 1555 2.05 SSBOND 12 CYS M 76 CYS M 94 1555 1555 2.13 CISPEP 1 THR N 6 PRO N 7 0 -2.18 CISPEP 2 THR O 6 PRO O 7 0 -3.92 CRYST1 73.979 82.719 107.363 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 0.013517 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012089 0.000000 0.00000 SCALE3 0.000000 0.000000 0.009314 0.00000