HEADER HYDROLASE/IMMUNE SYSTEM 27-MAY-08 3D9A TITLE HIGH RESOLUTION CRYSTAL STRUCTURE STRUCTURE OF HYHEL10 FAB COMPLEXED TITLE 2 TO HEN EGG LYSOZYME COMPND MOL_ID: 1; COMPND 2 MOLECULE: LYSOZYME C; COMPND 3 CHAIN: C; COMPND 4 SYNONYM: 1,4-BETA-N-ACETYLMURAMIDASE C, ALLERGEN GAL D 4, ALLERGEN COMPND 5 GAL D IV; COMPND 6 EC: 3.2.1.17; COMPND 7 MOL_ID: 2; COMPND 8 MOLECULE: LIGHT CHAIN OF HYHEL10 ANTIBODY FRAGMENT (FAB); COMPND 9 CHAIN: L; COMPND 10 ENGINEERED: YES; COMPND 11 MOL_ID: 3; COMPND 12 MOLECULE: HEAVY CHAIN OF HYHEL10 ANTIBODY FRAGMENT (FAB); COMPND 13 CHAIN: H; COMPND 14 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031; SOURCE 5 OTHER_DETAILS: EGG WHITE; SOURCE 6 MOL_ID: 2; SOURCE 7 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 8 ORGANISM_COMMON: MOUSE; SOURCE 9 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 10 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 11 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 12 EXPRESSION_SYSTEM_PLASMID: PET30; SOURCE 13 MOL_ID: 3; SOURCE 14 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 15 ORGANISM_COMMON: MOUSE; SOURCE 16 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 17 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 18 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 19 EXPRESSION_SYSTEM_PLASMID: PET30 KEYWDS LYSOZYME, HYHEL10, FAB, ANTIBODY, ANTIGEN, ALLERGEN, ANTIMICROBIAL, KEYWDS 2 BACTERIOLYTIC ENZYME, GLYCOSIDASE, HYDROLASE, HYDROLASE-IMMUNE KEYWDS 3 SYSTEM COMPLEX EXPDTA X-RAY DIFFRACTION AUTHOR M.E.DESANTIS,M.LI,A.SHANMUGANATHAN,M.ACCHIONE,R.WALTER,A.WLODAWER, AUTHOR 2 S.SMITH-GILL REVDAT 7 30-AUG-23 3D9A 1 DBREF REVDAT 6 25-OCT-17 3D9A 1 REMARK REVDAT 5 25-SEP-13 3D9A 1 REMARK REVDAT 4 13-JUL-11 3D9A 1 VERSN REVDAT 3 02-MAR-10 3D9A 1 JRNL REVDAT 2 24-FEB-09 3D9A 1 VERSN REVDAT 1 10-JUN-08 3D9A 0 JRNL AUTH M.ACCHIONE,C.A.LIPSCHULTZ,M.E.DESANTIS,A.SHANMUGANATHAN, JRNL AUTH 2 M.LI,A.WLODAWER,S.TARASOV,S.J.SMITH-GILL JRNL TITL LIGHT CHAIN SOMATIC MUTATIONS CHANGE THERMODYNAMICS OF JRNL TITL 2 BINDING AND WATER COORDINATION IN THE HYHEL-10 FAMILY OF JRNL TITL 3 ANTIBODIES. JRNL REF MOL.IMMUNOL. V. 47 457 2009 JRNL REFN ISSN 0161-5890 JRNL PMID 19781789 JRNL DOI 10.1016/J.MOLIMM.2009.08.018 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.4.0057 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 50.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.3 REMARK 3 NUMBER OF REFLECTIONS : 165981 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) : 0.191 REMARK 3 R VALUE (WORKING SET) : 0.190 REMARK 3 FREE R VALUE : 0.205 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.000 REMARK 3 FREE R VALUE TEST SET COUNT : 5014 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) : 1.20 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.23 REMARK 3 REFLECTION IN BIN (WORKING SET) : 11795 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 98.63 REMARK 3 BIN R VALUE (WORKING SET) : 0.2470 REMARK 3 BIN FREE R VALUE SET COUNT : 352 REMARK 3 BIN FREE R VALUE : 0.2750 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 4253 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 683 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) : 15.28 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.31000 REMARK 3 B22 (A**2) : 0.35000 REMARK 3 B33 (A**2) : -0.63000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.09000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.043 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.044 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.029 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.299 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.962 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.957 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 4377 ; 0.011 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): 2904 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 5975 ; 1.456 ; 1.934 REMARK 3 BOND ANGLES OTHERS (DEGREES): 7068 ; 0.916 ; 3.005 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 555 ; 8.607 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 184 ;36.032 ;24.185 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 690 ;13.275 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 22 ;18.048 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 664 ; 0.092 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 4911 ; 0.007 ; 0.021 REMARK 3 GENERAL PLANES OTHERS (A): 883 ; 0.001 ; 0.020 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): 2755 ; 0.828 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 1117 ; 0.210 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 4471 ; 1.575 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 1622 ; 2.279 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 1501 ; 3.390 ; 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 : 5 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 : C 601 C 729 REMARK 3 ORIGIN FOR THE GROUP (A): 5.4752 8.2174 12.6465 REMARK 3 T TENSOR REMARK 3 T11: -0.0294 T22: 0.0082 REMARK 3 T33: -0.0336 T12: 0.0187 REMARK 3 T13: 0.0020 T23: 0.0037 REMARK 3 L TENSOR REMARK 3 L11: 0.3658 L22: 0.6560 REMARK 3 L33: 1.4603 L12: 0.1445 REMARK 3 L13: 0.0574 L23: 0.0197 REMARK 3 S TENSOR REMARK 3 S11: 0.0519 S12: 0.1287 S13: 0.0021 REMARK 3 S21: -0.0051 S22: -0.0439 S23: -0.0035 REMARK 3 S31: 0.0841 S32: -0.0513 S33: -0.0080 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 107 REMARK 3 ORIGIN FOR THE GROUP (A): 3.8468 19.7158 38.7346 REMARK 3 T TENSOR REMARK 3 T11: -0.0156 T22: -0.0387 REMARK 3 T33: -0.0001 T12: -0.0059 REMARK 3 T13: -0.0008 T23: -0.0088 REMARK 3 L TENSOR REMARK 3 L11: 0.7312 L22: 0.8899 REMARK 3 L33: 1.0436 L12: -0.7102 REMARK 3 L13: -0.1214 L23: 0.2975 REMARK 3 S TENSOR REMARK 3 S11: -0.0606 S12: -0.0226 S13: 0.0701 REMARK 3 S21: 0.0698 S22: 0.0515 S23: -0.0344 REMARK 3 S31: -0.0151 S32: -0.0726 S33: 0.0091 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 : L 108 L 213 REMARK 3 ORIGIN FOR THE GROUP (A): 11.2517 20.7725 75.1895 REMARK 3 T TENSOR REMARK 3 T11: -0.0337 T22: 0.0691 REMARK 3 T33: -0.0641 T12: 0.0512 REMARK 3 T13: 0.0397 T23: 0.0479 REMARK 3 L TENSOR REMARK 3 L11: 1.2427 L22: 0.8892 REMARK 3 L33: 1.7871 L12: -0.4403 REMARK 3 L13: 1.0594 L23: -0.0315 REMARK 3 S TENSOR REMARK 3 S11: 0.0850 S12: 0.0389 S13: 0.0561 REMARK 3 S21: -0.1104 S22: -0.1062 S23: -0.0873 REMARK 3 S31: -0.1327 S32: 0.1432 S33: 0.0212 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 : H 301 H 412 REMARK 3 ORIGIN FOR THE GROUP (A): 16.2943 1.5189 39.7038 REMARK 3 T TENSOR REMARK 3 T11: -0.0205 T22: -0.0426 REMARK 3 T33: -0.0030 T12: -0.0098 REMARK 3 T13: -0.0089 T23: 0.0081 REMARK 3 L TENSOR REMARK 3 L11: 0.5930 L22: 0.6812 REMARK 3 L33: 1.3512 L12: -0.4632 REMARK 3 L13: 0.2975 L23: -0.4807 REMARK 3 S TENSOR REMARK 3 S11: 0.0133 S12: -0.0235 S13: -0.0137 REMARK 3 S21: 0.0039 S22: 0.0057 S23: -0.0152 REMARK 3 S31: 0.0314 S32: 0.0481 S33: -0.0190 REMARK 3 REMARK 3 TLS GROUP : 5 REMARK 3 NUMBER OF COMPONENTS GROUP : 1 REMARK 3 COMPONENTS C SSSEQI TO C SSSEQI REMARK 3 RESIDUE RANGE : H 413 H 509 REMARK 3 ORIGIN FOR THE GROUP (A): 7.8833 5.8305 71.9497 REMARK 3 T TENSOR REMARK 3 T11: -0.0223 T22: 0.0516 REMARK 3 T33: -0.0615 T12: 0.0780 REMARK 3 T13: 0.0100 T23: 0.0132 REMARK 3 L TENSOR REMARK 3 L11: 0.7934 L22: 1.1271 REMARK 3 L33: 1.7749 L12: -0.1398 REMARK 3 L13: -0.9347 L23: 0.8321 REMARK 3 S TENSOR REMARK 3 S11: -0.0059 S12: 0.0535 S13: -0.0951 REMARK 3 S21: -0.0618 S22: -0.0958 S23: 0.0505 REMARK 3 S31: 0.1249 S32: -0.0503 S33: 0.1016 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: NULL REMARK 4 REMARK 4 3D9A COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 28-MAY-08. REMARK 100 THE DEPOSITION ID IS D_1000047753. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 22-APR-08 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-BM REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.000 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 225 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 166019 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 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 (%) : 99.4 REMARK 200 DATA REDUNDANCY : 4.100 REMARK 200 R MERGE (I) : 0.03900 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 12.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.23 REMARK 200 COMPLETENESS FOR SHELL (%) : 100.0 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.58000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : NULL 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 1NDM REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 45.41 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.25 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2M DI-AMMONIUM CITRATE; 20% PEG REMARK 280 3350, PH 7, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 38.69250 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TRIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 3450 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 19060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -24.0 KCAL/MOL REMARK 350 APPLY THE FOLLOWING TO CHAINS: C, L, H 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 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 C LEU C 617 O HOH C 824 1.53 REMARK 500 O LEU C 617 O HOH C 824 1.53 REMARK 500 CB SER L 7 O HOH L 455 1.58 REMARK 500 N GLY H 406 O HOH H 644 1.61 REMARK 500 O HOH L 364 O HOH L 368 1.68 REMARK 500 O LEU C 617 O HOH C 805 1.72 REMARK 500 OE1 GLU H 306 O HOH H 644 1.80 REMARK 500 CB SER L 176 O HOH L 454 1.82 REMARK 500 N ASP C 618 O HOH C 824 1.85 REMARK 500 O GLN H 405 O HOH H 605 1.87 REMARK 500 OG SER L 28 O HOH L 366 1.92 REMARK 500 O HOH C 758 O HOH C 847 1.92 REMARK 500 O HOH H 621 O HOH H 649 1.94 REMARK 500 OD1 ASP C 618 O HOH C 806 1.97 REMARK 500 OD1 ASN C 703 O HOH C 749 2.00 REMARK 500 OH TYR C 623 O HOH C 872 2.01 REMARK 500 O ASP H 301 O HOH H 647 2.03 REMARK 500 OD1 ASN C 665 O HOH C 868 2.04 REMARK 500 ND2 ASN H 397 OD2 ASP H 401 2.04 REMARK 500 ND2 ASN C 703 O HOH C 782 2.07 REMARK 500 CB ASN H 376 O HOH H 721 2.07 REMARK 500 OD1 ASN L 190 O HOH L 346 2.08 REMARK 500 O HOH L 339 O HOH L 364 2.10 REMARK 500 OG SER L 176 O HOH L 454 2.16 REMARK 500 O HOH H 726 O HOH H 762 2.17 REMARK 500 CA ASP C 618 O HOH C 824 2.17 REMARK 500 O HOH L 289 O HOH H 649 2.17 REMARK 500 O HOH H 533 O HOH H 729 2.17 REMARK 500 ND2 ASN C 703 O HOH C 749 2.18 REMARK 500 O HOH H 649 O HOH H 696 2.19 REMARK 500 O SER L 40 O HOH L 441 2.19 REMARK 500 O ASP C 618 O HOH C 745 2.19 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 O HOH L 469 O HOH H 538 2656 1.98 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 L 211 NE - CZ - NH2 ANGL. DEV. = 3.8 DEGREES REMARK 500 ALA H 498 N - CA - C ANGL. DEV. = 18.4 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 L 51 -42.77 76.22 REMARK 500 SER L 52 -2.02 -144.43 REMARK 500 SER H 315 -2.76 79.55 REMARK 500 ASP H 327 106.34 -162.47 REMARK 500 SER H 365 -7.15 89.98 REMARK 500 ASN H 376 54.87 38.19 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 VAL H 497 ALA H 498 134.23 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1NDM RELATED DB: PDB REMARK 900 HYHEL26 FAB COMPLEXED TO LYSOZYME REMARK 900 RELATED ID: 3HFM RELATED DB: PDB REMARK 900 3.0 ANGSTROM CRYSTAL STRUCTURE OF HYHEL10 FAB COMPLEXED TO LYSOZYME DBREF 3D9A C 601 729 UNP P00698 LYSC_CHICK 19 147 DBREF 3D9A L 1 213 PDB 3D9A 3D9A 1 213 DBREF 3D9A H 301 510 PDB 3D9A 3D9A 301 510 SEQRES 1 C 129 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS SEQRES 2 C 129 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY SEQRES 3 C 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN SEQRES 4 C 129 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP SEQRES 5 C 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN SEQRES 6 C 129 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE SEQRES 7 C 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER SEQRES 8 C 129 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY SEQRES 9 C 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY SEQRES 10 C 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU SEQRES 1 L 213 ASP ILE VAL LEU THR GLN SER PRO ALA THR LEU SER VAL SEQRES 2 L 213 THR PRO GLY ASN SER VAL SER LEU SER CYS ARG ALA SER SEQRES 3 L 213 GLN SER ILE GLY ASN ASN LEU HIS TRP TYR GLN GLN LYS SEQRES 4 L 213 SER HIS GLU SER PRO ARG LEU LEU ILE LYS TYR ALA SER SEQRES 5 L 213 GLN SER ILE SER GLY ILE PRO SER ARG PHE SER GLY SER SEQRES 6 L 213 GLY SER GLY THR ASP PHE THR LEU SER ILE ASN SER VAL SEQRES 7 L 213 GLU THR GLU ASP PHE GLY MET TYR PHE CYS GLN GLN SER SEQRES 8 L 213 ASN SER TRP PRO TYR THR PHE GLY GLY GLY THR LYS LEU SEQRES 9 L 213 GLU ILE LYS ARG ALA ASP ALA ALA PRO THR VAL SER ILE SEQRES 10 L 213 PHE PRO PRO SER SER GLU GLN LEU THR SER GLY GLY ALA SEQRES 11 L 213 SER VAL VAL CYS PHE LEU ASN ASN PHE TYR PRO LYS ASP SEQRES 12 L 213 ILE ASN VAL LYS TRP LYS ILE ASP GLY SER GLU ARG GLN SEQRES 13 L 213 ASN GLY VAL LEU ASN SER TRP THR ASP GLN ASP SER LYS SEQRES 14 L 213 ASP SER THR TYR SER MET SER SER THR LEU THR LEU THR SEQRES 15 L 213 LYS ASP GLU TYR GLU ARG HIS ASN SER TYR THR CYS GLU SEQRES 16 L 213 ALA THR HIS LYS THR SER THR SER PRO ILE VAL LYS SER SEQRES 17 L 213 PHE ASN ARG ASN GLU SEQRES 1 H 210 ASP VAL GLN LEU GLN GLU SER GLY PRO SER LEU VAL LYS SEQRES 2 H 210 PRO SER GLN THR LEU SER LEU THR CYS SER VAL THR GLY SEQRES 3 H 210 ASP SER ILE THR SER ASP TYR TRP SER TRP ILE ARG LYS SEQRES 4 H 210 PHE PRO GLY ASN ARG LEU GLU TYR MET GLY TYR VAL SER SEQRES 5 H 210 TYR SER GLY SER THR TYR TYR ASN PRO SER LEU LYS SER SEQRES 6 H 210 ARG ILE SER ILE THR ARG ASP THR SER LYS ASN GLN TYR SEQRES 7 H 210 TYR LEU ASP LEU ASN SER VAL THR THR GLU ASP THR ALA SEQRES 8 H 210 THR TYR TYR CYS ALA ASN TRP ASP GLY ASP TYR TRP GLY SEQRES 9 H 210 GLN GLY THR LEU VAL THR VAL SER ALA ALA LYS THR THR SEQRES 10 H 210 PRO PRO SER VAL TYR PRO LEU ALA PRO GLY SER ALA ALA SEQRES 11 H 210 GLN THR ASN SER MET VAL THR LEU GLY CYS LEU VAL LYS SEQRES 12 H 210 GLY TYR PHE PRO GLU PRO VAL THR VAL THR TRP ASN SER SEQRES 13 H 210 GLY SER LEU SER SER GLY VAL HIS THR PHE PRO ALA VAL SEQRES 14 H 210 LEU GLN SER ASP LEU TYR THR LEU SER SER SER VAL THR SEQRES 15 H 210 VAL PRO SER SER THR TRP PRO SER GLU THR VAL THR CYS SEQRES 16 H 210 ASN VAL ALA HIS PRO ALA SER SER THR LYS VAL ASP LYS SEQRES 17 H 210 LYS ILE FORMUL 4 HOH *683(H2 O) HELIX 1 1 GLY C 604 HIS C 615 1 12 HELIX 2 2 ASN C 619 TYR C 623 5 5 HELIX 3 3 SER C 624 ASN C 637 1 14 HELIX 4 4 PRO C 679 SER C 685 5 7 HELIX 5 5 ILE C 688 SER C 700 1 13 HELIX 6 6 ASN C 703 ALA C 707 5 5 HELIX 7 7 TRP C 708 CYS C 715 1 8 HELIX 8 8 ASP C 719 ARG C 725 5 7 HELIX 9 9 GLU L 79 PHE L 83 5 5 HELIX 10 10 SER L 121 SER L 127 1 7 HELIX 11 11 LYS L 183 HIS L 189 1 7 HELIX 12 12 SER H 328 ASP H 332 5 5 HELIX 13 13 PRO H 361 LYS H 364 5 4 HELIX 14 14 THR H 373 LYS H 375 5 3 HELIX 15 15 THR H 386 THR H 390 5 5 HELIX 16 16 SER H 456 SER H 458 5 3 HELIX 17 17 SER H 486 TRP H 488 5 3 HELIX 18 18 PRO H 500 SER H 503 5 4 SHEET 1 A 3 THR C 643 ARG C 645 0 SHEET 2 A 3 THR C 651 TYR C 653 -1 O ASP C 652 N ASN C 644 SHEET 3 A 3 ILE C 658 ASN C 659 -1 O ILE C 658 N TYR C 653 SHEET 1 B 4 LEU L 4 SER L 7 0 SHEET 2 B 4 VAL L 19 ALA L 25 -1 O ARG L 24 N THR L 5 SHEET 3 B 4 ASP L 70 ILE L 75 -1 O LEU L 73 N LEU L 21 SHEET 4 B 4 PHE L 62 SER L 67 -1 N SER L 63 O SER L 74 SHEET 1 C 6 THR L 10 VAL L 13 0 SHEET 2 C 6 THR L 102 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 C 6 GLY L 84 GLN L 90 -1 N GLY L 84 O LEU L 104 SHEET 4 C 6 LEU L 33 GLN L 38 -1 N GLN L 38 O MET L 85 SHEET 5 C 6 ARG L 45 LYS L 49 -1 O LEU L 47 N TRP L 35 SHEET 6 C 6 GLN L 53 SER L 54 -1 O GLN L 53 N LYS L 49 SHEET 1 D 4 THR L 10 VAL L 13 0 SHEET 2 D 4 THR L 102 ILE L 106 1 O GLU L 105 N LEU L 11 SHEET 3 D 4 GLY L 84 GLN L 90 -1 N GLY L 84 O LEU L 104 SHEET 4 D 4 THR L 97 PHE L 98 -1 O THR L 97 N GLN L 90 SHEET 1 E 4 THR L 114 PHE L 118 0 SHEET 2 E 4 GLY L 129 PHE L 139 -1 O ASN L 137 N THR L 114 SHEET 3 E 4 TYR L 173 THR L 182 -1 O MET L 175 N LEU L 136 SHEET 4 E 4 VAL L 159 TRP L 163 -1 N SER L 162 O SER L 176 SHEET 1 F 4 SER L 153 ARG L 155 0 SHEET 2 F 4 ASN L 145 ILE L 150 -1 N ILE L 150 O SER L 153 SHEET 3 F 4 SER L 191 THR L 197 -1 O THR L 197 N ASN L 145 SHEET 4 F 4 ILE L 205 ASN L 210 -1 O LYS L 207 N CYS L 194 SHEET 1 G 4 GLN H 303 SER H 307 0 SHEET 2 G 4 LEU H 318 THR H 325 -1 O THR H 321 N SER H 307 SHEET 3 G 4 GLN H 377 LEU H 382 -1 O LEU H 382 N LEU H 318 SHEET 4 G 4 ILE H 367 ASP H 372 -1 N ASP H 372 O GLN H 377 SHEET 1 H 6 LEU H 311 VAL H 312 0 SHEET 2 H 6 THR H 407 VAL H 411 1 O THR H 410 N VAL H 312 SHEET 3 H 6 ALA H 391 ASN H 397 -1 N TYR H 393 O THR H 407 SHEET 4 H 6 TRP H 334 PHE H 340 -1 N ILE H 337 O TYR H 394 SHEET 5 H 6 ARG H 344 VAL H 351 -1 O ARG H 344 N PHE H 340 SHEET 6 H 6 THR H 357 TYR H 359 -1 O TYR H 358 N TYR H 350 SHEET 1 I 4 SER H 420 LEU H 424 0 SHEET 2 I 4 MET H 435 TYR H 445 -1 O LYS H 443 N SER H 420 SHEET 3 I 4 LEU H 474 PRO H 484 -1 O LEU H 477 N VAL H 442 SHEET 4 I 4 VAL H 463 THR H 465 -1 N HIS H 464 O SER H 480 SHEET 1 J 4 SER H 420 LEU H 424 0 SHEET 2 J 4 MET H 435 TYR H 445 -1 O LYS H 443 N SER H 420 SHEET 3 J 4 LEU H 474 PRO H 484 -1 O LEU H 477 N VAL H 442 SHEET 4 J 4 VAL H 469 GLN H 471 -1 N GLN H 471 O LEU H 474 SHEET 1 K 3 THR H 451 TRP H 454 0 SHEET 2 K 3 THR H 494 HIS H 499 -1 O ASN H 496 N THR H 453 SHEET 3 K 3 THR H 504 LYS H 509 -1 O VAL H 506 N VAL H 497 SSBOND 1 CYS C 606 CYS C 727 1555 1555 2.06 SSBOND 2 CYS C 630 CYS C 715 1555 1555 2.10 SSBOND 3 CYS C 664 CYS C 680 1555 1555 2.05 SSBOND 4 CYS C 676 CYS C 694 1555 1555 2.07 SSBOND 5 CYS L 23 CYS L 88 1555 1555 2.14 SSBOND 6 CYS L 134 CYS L 194 1555 1555 2.02 SSBOND 7 CYS H 322 CYS H 395 1555 1555 2.14 SSBOND 8 CYS H 440 CYS H 495 1555 1555 2.00 CISPEP 1 SER L 7 PRO L 8 0 -7.55 CISPEP 2 TRP L 94 PRO L 95 0 6.73 CISPEP 3 TYR L 140 PRO L 141 0 0.40 CISPEP 4 PHE H 446 PRO H 447 0 -9.38 CISPEP 5 GLU H 448 PRO H 449 0 -0.17 CISPEP 6 TRP H 488 PRO H 489 0 4.70 CRYST1 39.842 77.385 89.115 90.00 96.66 90.00 P 1 21 1 2 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 0.025099 0.000000 0.002929 0.00000 SCALE2 0.000000 0.012922 0.000000 0.00000 SCALE3 0.000000 0.000000 0.011298 0.00000