HEADER HYDROLASE 30-OCT-99 1D9U TITLE BACTERIOPHAGE LAMBDA LYSOZYME COMPLEXED WITH A CHITOHEXASACHARIDE COMPND MOL_ID: 1; COMPND 2 MOLECULE: BACTERIOPHAGE LAMBDA LYSOZYME; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: LAL; COMPND 5 EC: 3.2.1.17; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: ENTEROBACTERIA PHAGE LAMBDA; SOURCE 3 ORGANISM_TAXID: 10710; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS GLYCOSIDASE, TRANSGLYCOSYLASE, LYSOZYME, SIX-SUGAR COMPLEX, HYDROLASE EXPDTA X-RAY DIFFRACTION AUTHOR A.K.W.LEUNG,H.S.DUEWEL,J.F.HONEK,A.M.BERGHUIS REVDAT 6 07-FEB-24 1D9U 1 HETSYN REVDAT 5 29-JUL-20 1D9U 1 COMPND REMARK HETNAM LINK REVDAT 5 2 1 SITE ATOM REVDAT 4 13-JUL-11 1D9U 1 VERSN REVDAT 3 24-FEB-09 1D9U 1 VERSN REVDAT 2 01-APR-03 1D9U 1 JRNL REVDAT 1 23-MAY-01 1D9U 0 JRNL AUTH A.K.LEUNG,H.S.DUEWEL,J.F.HONEK,A.M.BERGHUIS JRNL TITL CRYSTAL STRUCTURE OF THE LYTIC TRANSGLYCOSYLASE FROM JRNL TITL 2 BACTERIOPHAGE LAMBDA IN COMPLEX WITH JRNL TITL 3 HEXA-N-ACETYLCHITOHEXAOSE. JRNL REF BIOCHEMISTRY V. 40 5665 2001 JRNL REFN ISSN 0006-2960 JRNL PMID 11341831 JRNL DOI 10.1021/BI0028035 REMARK 2 REMARK 2 RESOLUTION. 2.60 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR 3.843 REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.60 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 40.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 2.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 1000000.000 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 NUMBER OF REFLECTIONS : 9906 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 SET) : 0.226 REMARK 3 FREE R VALUE : 0.287 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.300 REMARK 3 FREE R VALUE TEST SET COUNT : 1025 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.009 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.60 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.76 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 24.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 476 REMARK 3 BIN R VALUE (WORKING SET) : 0.2670 REMARK 3 BIN FREE R VALUE : 0.3200 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 12.30 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 67 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.039 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 2448 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 190 REMARK 3 SOLVENT ATOMS : 31 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 27.30 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.44000 REMARK 3 B22 (A**2) : -0.55000 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.29 REMARK 3 ESD FROM SIGMAA (A) : 0.04 REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.41 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.30 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.466 REMARK 3 BOND ANGLES (DEGREES) : 6.200 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 21.70 REMARK 3 IMPROPER ANGLES (DEGREES) : 0.960 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 4.310 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 6.400 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 6.780 ; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 9.430 ; 2.500 REMARK 3 REMARK 3 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: WHILE ALL OBSERVED DATA OUT TO 2.6 REMARK 3 ANGSTROM HAS BEEN USED IN REFINEMENT, THE NOMINAL RESOLUTION OF REMARK 3 THE STRUCTURE IS 2.8 ANGSTROM REMARK 4 REMARK 4 1D9U COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 02-NOV-99. REMARK 100 THE DEPOSITION ID IS D_1000009924. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 30-AUG-96 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 4.7 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS II REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14138 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.600 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 92.0 REMARK 200 DATA REDUNDANCY : 7.700 REMARK 200 R MERGE (I) : 0.11800 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 7.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.60 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.69 REMARK 200 COMPLETENESS FOR SHELL (%) : 55.3 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.50700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 59.98 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 3.07 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 2000 MME, AMMONIUM SULFATE, PH REMARK 280 4.7, MICRODIALYSIS, TEMPERATURE 298K 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 28.60000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 61.22350 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 30.54050 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 61.22350 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 28.60000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 30.54050 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, C, D 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: 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 ARG A 25 -70.22 -82.57 REMARK 500 ASN A 30 65.37 -157.96 REMARK 500 LEU A 55 -84.12 -65.65 REMARK 500 PRO A 57 -19.51 -40.96 REMARK 500 LEU A 59 122.36 176.31 REMARK 500 GLN A 68 71.91 37.07 REMARK 500 VAL A 153 -169.88 -117.38 REMARK 500 ASP B 22 71.72 -118.25 REMARK 500 HIS B 31 48.20 35.51 REMARK 500 LEU B 55 -94.19 -68.31 REMARK 500 PRO B 57 -8.71 -45.35 REMARK 500 GLN B 68 58.03 39.99 REMARK 500 PHE B 86 49.64 -108.95 REMARK 500 HIS B 137 -178.71 -69.79 REMARK 500 REMARK 500 REMARK: NULL DBREF 1D9U A 1 154 UNP P03706 LYS_LAMBD 1 154 DBREF 1D9U B 1 154 UNP P03706 LYS_LAMBD 1 154 SEQRES 1 A 154 MET VAL GLU ILE ASN ASN GLN ARG LYS ALA PHE LEU ASP SEQRES 2 A 154 MET LEU ALA TRP SER GLU GLY THR ASP ASN GLY ARG GLN SEQRES 3 A 154 LYS THR ARG ASN HIS GLY TYR ASP VAL ILE VAL GLY GLY SEQRES 4 A 154 GLU LEU PHE THR ASP TYR SER ASP HIS PRO ARG LYS LEU SEQRES 5 A 154 VAL THR LEU ASN PRO LYS LEU LYS SER THR GLY ALA GLY SEQRES 6 A 154 ARG TYR GLN LEU LEU SER ARG TRP TRP ASP ALA TYR ARG SEQRES 7 A 154 LYS GLN LEU GLY LEU LYS ASP PHE SER PRO LYS SER GLN SEQRES 8 A 154 ASP ALA VAL ALA LEU GLN GLN ILE LYS GLU ARG GLY ALA SEQRES 9 A 154 LEU PRO MET ILE ASP ARG GLY ASP ILE ARG GLN ALA ILE SEQRES 10 A 154 ASP ARG CYS SER ASN ILE TRP ALA SER LEU PRO GLY ALA SEQRES 11 A 154 GLY TYR GLY GLN PHE GLU HIS LYS ALA ASP SER LEU ILE SEQRES 12 A 154 ALA LYS PHE LYS GLU ALA GLY GLY THR VAL ARG SEQRES 1 B 154 MET VAL GLU ILE ASN ASN GLN ARG LYS ALA PHE LEU ASP SEQRES 2 B 154 MET LEU ALA TRP SER GLU GLY THR ASP ASN GLY ARG GLN SEQRES 3 B 154 LYS THR ARG ASN HIS GLY TYR ASP VAL ILE VAL GLY GLY SEQRES 4 B 154 GLU LEU PHE THR ASP TYR SER ASP HIS PRO ARG LYS LEU SEQRES 5 B 154 VAL THR LEU ASN PRO LYS LEU LYS SER THR GLY ALA GLY SEQRES 6 B 154 ARG TYR GLN LEU LEU SER ARG TRP TRP ASP ALA TYR ARG SEQRES 7 B 154 LYS GLN LEU GLY LEU LYS ASP PHE SER PRO LYS SER GLN SEQRES 8 B 154 ASP ALA VAL ALA LEU GLN GLN ILE LYS GLU ARG GLY ALA SEQRES 9 B 154 LEU PRO MET ILE ASP ARG GLY ASP ILE ARG GLN ALA ILE SEQRES 10 B 154 ASP ARG CYS SER ASN ILE TRP ALA SER LEU PRO GLY ALA SEQRES 11 B 154 GLY TYR GLY GLN PHE GLU HIS LYS ALA ASP SER LEU ILE SEQRES 12 B 154 ALA LYS PHE LYS GLU ALA GLY GLY THR VAL ARG HET NAG C 1 15 HET NAG C 2 14 HET NDG C 3 14 HET NAG C 4 14 HET NAG C 5 14 HET NAG C 6 14 HET NAG D 1 15 HET NAG D 2 14 HET NAG D 3 14 HET NDG D 4 14 HET NDG D 5 14 HET NAG D 6 14 HET SO4 A 200 5 HET SO4 A 201 5 HET SO4 A 203 5 HET SO4 B 202 5 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE HETNAM NDG 2-ACETAMIDO-2-DEOXY-ALPHA-D-GLUCOPYRANOSE HETNAM SO4 SULFATE ION HETSYN NAG N-ACETYL-BETA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY-BETA- HETSYN 2 NAG D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2-ACETAMIDO- HETSYN 3 NAG 2-DEOXY-GLUCOSE; N-ACETYL-D-GLUCOSAMINE HETSYN NDG N-ACETYL-ALPHA-D-GLUCOSAMINE; 2-ACETAMIDO-2-DEOXY- HETSYN 2 NDG ALPHA-D-GLUCOSE; 2-ACETAMIDO-2-DEOXY-D-GLUCOSE; 2- HETSYN 3 NDG ACETAMIDO-2-DEOXY-GLUCOSE; 2-(ACETYLAMINO)-2-DEOXY-A- HETSYN 4 NDG D-GLUCOPYRANOSE FORMUL 3 NAG 9(C8 H15 N O6) FORMUL 3 NDG 3(C8 H15 N O6) FORMUL 5 SO4 4(O4 S 2-) FORMUL 9 HOH *31(H2 O) HELIX 1 1 ASN A 5 GLU A 19 1 15 HELIX 2 2 LEU A 70 LEU A 81 1 12 HELIX 3 3 SER A 87 ARG A 102 1 16 HELIX 4 4 ALA A 104 GLY A 111 1 8 HELIX 5 5 ASP A 112 CYS A 120 1 9 HELIX 6 6 LYS A 138 GLU A 148 1 11 HELIX 7 7 ASN B 5 GLU B 19 1 15 HELIX 8 8 LEU B 70 GLY B 82 1 13 HELIX 9 9 SER B 87 ARG B 102 1 16 HELIX 10 10 ALA B 104 ARG B 110 1 7 HELIX 11 11 ASP B 112 SER B 121 1 10 HELIX 12 12 LYS B 138 GLU B 148 1 11 SHEET 1 A 2 VAL A 53 ASN A 56 0 SHEET 2 A 2 LEU A 59 SER A 61 -1 N LEU A 59 O ASN A 56 SHEET 1 B 2 VAL B 53 THR B 54 0 SHEET 2 B 2 LYS B 60 SER B 61 -1 N SER B 61 O VAL B 53 LINK O4 NAG C 1 C1 NAG C 2 1555 1555 1.39 LINK O4 NAG C 2 C1 NDG C 3 1555 1555 1.38 LINK O4 NDG C 3 C1 NAG C 4 1555 1555 1.39 LINK O4 NAG C 4 C1 NAG C 5 1555 1555 1.38 LINK O4 NAG C 5 C1 NAG C 6 1555 1555 1.39 LINK O4 NAG D 1 C1 NAG D 2 1555 1555 1.39 LINK O4 NAG D 2 C1 NAG D 3 1555 1555 1.38 LINK O4 NAG D 3 C1 NDG D 4 1555 1555 1.38 LINK O4 NDG D 4 C1 NDG D 5 1555 1555 1.39 LINK O4 NDG D 5 C1 NAG D 6 1555 1555 1.40 CRYST1 57.200 61.081 122.447 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 0.017483 0.000000 0.000000 0.00000 SCALE2 0.000000 0.016372 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008167 0.00000