HEADER HYDROLASE 14-DEC-14 4XAD
TITLE CRYSTAL STRUCTURE OF HEN EGG WHITE LYSOZYME IN COMPLEX WITH GALF-
TITLE 2 GLCNAC
COMPND MOL_ID: 1;
COMPND 2 MOLECULE: LYSOZYME C;
COMPND 3 CHAIN: A;
COMPND 4 SYNONYM: 1,4-BETA-N-ACETYLMURAMIDASE C,ALLERGEN GAL D IV;
COMPND 5 EC: 3.2.1.17
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
KEYWDS GALACTOFURANOSE, GALF-GLCNAC, PROTEIN-CARBOHYDRATE COMPLEX,
KEYWDS 2 TRYPANOSOMA CRUZI O-LINKED DISACCHARIDE, HYDROLASE
EXPDTA X-RAY DIFFRACTION
AUTHOR K.WANGKANONT,L.L.KIESSLING
REVDAT 4 27-SEP-23 4XAD 1 HETSYN
REVDAT 3 29-JUL-20 4XAD 1 COMPND REMARK HET HETNAM
REVDAT 3 2 1 HETSYN FORMUL LINK SITE
REVDAT 3 3 1 ATOM
REVDAT 2 22-NOV-17 4XAD 1 SOURCE KEYWDS REMARK
REVDAT 1 31-DEC-14 4XAD 0
JRNL AUTH K.WANGKANONT,L.L.KIESSLING
JRNL TITL CRYSTAL STRUCTURE OF HEN EGG WHITE LYSOZYME IN COMPLEX WITH
JRNL TITL 2 GALF-GLCNAC, AN O-LINKED DISACCHARIDE CORE FROM TRYPANOSOMA
JRNL TITL 3 CRUZI
JRNL REF TO BE PUBLISHED
JRNL REFN
REMARK 2
REMARK 2 RESOLUTION. 1.25 ANGSTROMS.
REMARK 3
REMARK 3 REFINEMENT.
REMARK 3 PROGRAM : PHENIX
REMARK 3 AUTHORS : PAUL ADAMS,PAVEL AFONINE,VINCENT CHEN,IAN
REMARK 3 : DAVIS,KRESHNA GOPAL,RALF GROSSE-KUNSTLEVE,
REMARK 3 : LI-WEI HUNG,ROBERT IMMORMINO,TOM IOERGER,
REMARK 3 : AIRLIE MCCOY,ERIK MCKEE,NIGEL MORIARTY,
REMARK 3 : REETAL PAI,RANDY READ,JANE RICHARDSON,
REMARK 3 : DAVID RICHARDSON,TOD ROMO,JIM SACCHETTINI,
REMARK 3 : NICHOLAS SAUTER,JACOB SMITH,LAURENT
REMARK 3 : STORONI,TOM TERWILLIGER,PETER ZWART
REMARK 3
REMARK 3 REFINEMENT TARGET : ML
REMARK 3
REMARK 3 DATA USED IN REFINEMENT.
REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.25
REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 27.11
REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.960
REMARK 3 COMPLETENESS FOR RANGE (%) : 99.5
REMARK 3 NUMBER OF REFLECTIONS : NULL
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT.
REMARK 3 R VALUE (WORKING + TEST SET) : 0.141
REMARK 3 R VALUE (WORKING SET) : 0.140
REMARK 3 FREE R VALUE : 0.168
REMARK 3 FREE R VALUE TEST SET SIZE (%) : 4.850
REMARK 3 FREE R VALUE TEST SET COUNT : 2975
REMARK 3
REMARK 3 FIT TO DATA USED IN REFINEMENT (IN BINS).
REMARK 3 BIN RESOLUTION RANGE COMPL. NWORK NFREE RWORK RFREE
REMARK 3 1 27.1159 - 2.6906 1.00 5903 255 0.1514 0.1796
REMARK 3 2 2.6906 - 2.1359 1.00 5904 276 0.1498 0.1708
REMARK 3 3 2.1359 - 1.8659 1.00 5872 275 0.1364 0.1614
REMARK 3 4 1.8659 - 1.6954 1.00 5835 306 0.1315 0.1646
REMARK 3 5 1.6954 - 1.5739 1.00 5862 298 0.1162 0.1537
REMARK 3 6 1.5739 - 1.4811 1.00 5923 304 0.1113 0.1290
REMARK 3 7 1.4811 - 1.4069 1.00 5829 291 0.1240 0.1754
REMARK 3 8 1.4069 - 1.3457 1.00 5848 321 0.1239 0.1681
REMARK 3 9 1.3457 - 1.2939 1.00 5788 342 0.1361 0.1587
REMARK 3 10 1.2939 - 1.2492 0.95 5597 307 0.1573 0.1932
REMARK 3
REMARK 3 BULK SOLVENT MODELLING.
REMARK 3 METHOD USED : FLAT BULK SOLVENT MODEL
REMARK 3 SOLVENT RADIUS : 1.11
REMARK 3 SHRINKAGE RADIUS : 0.90
REMARK 3 K_SOL : NULL
REMARK 3 B_SOL : NULL
REMARK 3
REMARK 3 ERROR ESTIMATES.
REMARK 3 COORDINATE ERROR (MAXIMUM-LIKELIHOOD BASED) : 0.090
REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 12.670
REMARK 3
REMARK 3 B VALUES.
REMARK 3 FROM WILSON PLOT (A**2) : 12.99
REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.11
REMARK 3 OVERALL ANISOTROPIC B VALUE.
REMARK 3 B11 (A**2) : NULL
REMARK 3 B22 (A**2) : NULL
REMARK 3 B33 (A**2) : NULL
REMARK 3 B12 (A**2) : NULL
REMARK 3 B13 (A**2) : NULL
REMARK 3 B23 (A**2) : NULL
REMARK 3
REMARK 3 TWINNING INFORMATION.
REMARK 3 FRACTION: NULL
REMARK 3 OPERATOR: NULL
REMARK 3
REMARK 3 DEVIATIONS FROM IDEAL VALUES.
REMARK 3 RMSD COUNT
REMARK 3 BOND : 0.005 1163
REMARK 3 ANGLE : 1.013 1577
REMARK 3 CHIRALITY : 0.072 166
REMARK 3 PLANARITY : 0.003 208
REMARK 3 DIHEDRAL : 14.145 476
REMARK 3
REMARK 3 TLS DETAILS
REMARK 3 NUMBER OF TLS GROUPS : NULL
REMARK 3
REMARK 3 NCS DETAILS
REMARK 3 NUMBER OF NCS GROUPS : NULL
REMARK 3
REMARK 3 OTHER REFINEMENT REMARKS: NULL
REMARK 4
REMARK 4 4XAD COMPLIES WITH FORMAT V. 3.30, 13-JUL-11
REMARK 100
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 19-DEC-14.
REMARK 100 THE DEPOSITION ID IS D_1000205339.
REMARK 200
REMARK 200 EXPERIMENTAL DETAILS
REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION
REMARK 200 DATE OF DATA COLLECTION : 05-NOV-14
REMARK 200 TEMPERATURE (KELVIN) : 100
REMARK 200 PH : 4.6
REMARK 200 NUMBER OF CRYSTALS USED : 1
REMARK 200
REMARK 200 SYNCHROTRON (Y/N) : Y
REMARK 200 RADIATION SOURCE : APS
REMARK 200 BEAMLINE : 21-ID-D
REMARK 200 X-RAY GENERATOR MODEL : NULL
REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M
REMARK 200 WAVELENGTH OR RANGE (A) : 0.97904
REMARK 200 MONOCHROMATOR : SI(111)
REMARK 200 OPTICS : NULL
REMARK 200
REMARK 200 DETECTOR TYPE : CCD
REMARK 200 DETECTOR MANUFACTURER : RAYONIX MX-300
REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL
REMARK 200 DATA SCALING SOFTWARE : SCALEPACK
REMARK 200
REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 32700
REMARK 200 RESOLUTION RANGE HIGH (A) : 1.250
REMARK 200 RESOLUTION RANGE LOW (A) : 30.400
REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL
REMARK 200
REMARK 200 OVERALL.
REMARK 200 COMPLETENESS FOR RANGE (%) : 99.5
REMARK 200 DATA REDUNDANCY : 28.00
REMARK 200 R MERGE (I) : 0.08900
REMARK 200 R SYM (I) : NULL
REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 11.8000
REMARK 200
REMARK 200 IN THE HIGHEST RESOLUTION SHELL.
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.25
REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.29
REMARK 200 COMPLETENESS FOR SHELL (%) : 95.5
REMARK 200 DATA REDUNDANCY IN SHELL : 24.50
REMARK 200 R MERGE FOR SHELL (I) : 0.49200
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: MOLECULAR REPLACEMENT
REMARK 200 SOFTWARE USED: PHASER 2.5.2
REMARK 200 STARTING MODEL: 194L
REMARK 200
REMARK 200 REMARK: NULL
REMARK 280
REMARK 280 CRYSTAL
REMARK 280 SOLVENT CONTENT, VS (%): 38.54
REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.00
REMARK 280
REMARK 280 CRYSTALLIZATION CONDITIONS: 100 MM NAOAC, 1.5 M NACL, PH 4.6,
REMARK 280 VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K
REMARK 290
REMARK 290 CRYSTALLOGRAPHIC SYMMETRY
REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 43 21 2
REMARK 290
REMARK 290 SYMOP SYMMETRY
REMARK 290 NNNMMM OPERATOR
REMARK 290 1555 X,Y,Z
REMARK 290 2555 -X,-Y,Z+1/2
REMARK 290 3555 -Y+1/2,X+1/2,Z+3/4
REMARK 290 4555 Y+1/2,-X+1/2,Z+1/4
REMARK 290 5555 -X+1/2,Y+1/2,-Z+3/4
REMARK 290 6555 X+1/2,-Y+1/2,-Z+1/4
REMARK 290 7555 Y,X,-Z
REMARK 290 8555 -Y,-X,-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 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 18.85450
REMARK 290 SMTRY1 3 0.000000 -1.000000 0.000000 39.00100
REMARK 290 SMTRY2 3 1.000000 0.000000 0.000000 39.00100
REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 28.28175
REMARK 290 SMTRY1 4 0.000000 1.000000 0.000000 39.00100
REMARK 290 SMTRY2 4 -1.000000 0.000000 0.000000 39.00100
REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 9.42725
REMARK 290 SMTRY1 5 -1.000000 0.000000 0.000000 39.00100
REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 39.00100
REMARK 290 SMTRY3 5 0.000000 0.000000 -1.000000 28.28175
REMARK 290 SMTRY1 6 1.000000 0.000000 0.000000 39.00100
REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 39.00100
REMARK 290 SMTRY3 6 0.000000 0.000000 -1.000000 9.42725
REMARK 290 SMTRY1 7 0.000000 1.000000 0.000000 0.00000
REMARK 290 SMTRY2 7 1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 0.00000
REMARK 290 SMTRY1 8 0.000000 -1.000000 0.000000 0.00000
REMARK 290 SMTRY2 8 -1.000000 0.000000 0.000000 0.00000
REMARK 290 SMTRY3 8 0.000000 0.000000 -1.000000 18.85450
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 300 REMARK: BIOLOGICAL UNIT IS THE SAME AS ASYM.
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 TOTAL BURIED SURFACE AREA: 770 ANGSTROM**2
REMARK 350 SURFACE AREA OF THE COMPLEX: 6450 ANGSTROM**2
REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -56.0 KCAL/MOL
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, 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 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 A 350 LIES ON A SPECIAL POSITION.
REMARK 375 HOH A 415 LIES ON A SPECIAL POSITION.
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 HOH A 308 O HOH A 382 2.02
REMARK 500 O HOH A 433 O HOH A 447 2.02
REMARK 500 O HOH A 433 O HOH A 465 2.07
REMARK 500 NH2 ARG A 14 O HOH A 301 2.11
REMARK 500 OG SER A 85 O HOH A 461 2.16
REMARK 500 OD1 ASN A 93 O HOH A 455 2.17
REMARK 500 NZ LYS A 97 O HOH A 438 2.18
REMARK 500 O HOH A 303 O HOH A 386 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 A 301 O HOH A 301 8776 1.98
REMARK 500 O HOH A 305 O HOH A 308 7557 2.06
REMARK 500 O HOH A 330 O HOH A 382 7557 2.11
REMARK 500 O HOH A 318 O HOH A 318 7558 2.14
REMARK 500
REMARK 500 REMARK: NULL
DBREF 4XAD A 1 129 UNP P00698 LYSC_CHICK 19 147
SEQRES 1 A 129 LYS VAL PHE GLY ARG CYS GLU LEU ALA ALA ALA MET LYS
SEQRES 2 A 129 ARG HIS GLY LEU ASP ASN TYR ARG GLY TYR SER LEU GLY
SEQRES 3 A 129 ASN TRP VAL CYS ALA ALA LYS PHE GLU SER ASN PHE ASN
SEQRES 4 A 129 THR GLN ALA THR ASN ARG ASN THR ASP GLY SER THR ASP
SEQRES 5 A 129 TYR GLY ILE LEU GLN ILE ASN SER ARG TRP TRP CYS ASN
SEQRES 6 A 129 ASP GLY ARG THR PRO GLY SER ARG ASN LEU CYS ASN ILE
SEQRES 7 A 129 PRO CYS SER ALA LEU LEU SER SER ASP ILE THR ALA SER
SEQRES 8 A 129 VAL ASN CYS ALA LYS LYS ILE VAL SER ASP GLY ASN GLY
SEQRES 9 A 129 MET ASN ALA TRP VAL ALA TRP ARG ASN ARG CYS LYS GLY
SEQRES 10 A 129 THR ASP VAL GLN ALA TRP ILE ARG GLY CYS ARG LEU
HET NDG B 1 15
HET GZL B 2 11
HET CL A 201 1
HET CL A 202 1
HET CL A 203 1
HET CL A 204 1
HET CL A 205 1
HET CL A 206 1
HETNAM NDG 2-ACETAMIDO-2-DEOXY-ALPHA-D-GLUCOPYRANOSE
HETNAM GZL BETA-D-GALACTOFURANOSE
HETNAM CL CHLORIDE ION
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
HETSYN GZL BETA-D-GALACTOSE; D-GALACTOSE; GALACTOSE
FORMUL 2 NDG C8 H15 N O6
FORMUL 2 GZL C6 H12 O6
FORMUL 3 CL 6(CL 1-)
FORMUL 9 HOH *189(H2 O)
HELIX 1 AA1 GLY A 4 HIS A 15 1 12
HELIX 2 AA2 ASN A 19 TYR A 23 5 5
HELIX 3 AA3 SER A 24 ASN A 37 1 14
HELIX 4 AA4 PRO A 79 SER A 85 5 7
HELIX 5 AA5 ILE A 88 SER A 100 1 13
HELIX 6 AA6 ASN A 103 ALA A 107 5 5
HELIX 7 AA7 TRP A 108 CYS A 115 1 8
HELIX 8 AA8 ASP A 119 ARG A 125 5 7
SHEET 1 AA1 3 THR A 43 ARG A 45 0
SHEET 2 AA1 3 THR A 51 TYR A 53 -1 O ASP A 52 N ASN A 44
SHEET 3 AA1 3 ILE A 58 ASN A 59 -1 O ILE A 58 N TYR A 53
SSBOND 1 CYS A 6 CYS A 127 1555 1555 2.04
SSBOND 2 CYS A 30 CYS A 115 1555 1555 2.06
SSBOND 3 CYS A 64 CYS A 80 1555 1555 2.04
SSBOND 4 CYS A 76 CYS A 94 1555 1555 2.03
LINK O4 NDG B 1 C1 GZL B 2 1555 1555 1.42
CRYST1 78.002 78.002 37.709 90.00 90.00 90.00 P 43 21 2 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 0.012820 0.000000 0.000000 0.00000
SCALE2 0.000000 0.012820 0.000000 0.00000
SCALE3 0.000000 0.000000 0.026519 0.00000
(ATOM LINES ARE NOT SHOWN.)
END
