HEADER SUGAR BINDING PROTEIN 31-JUL-07 2QSK TITLE ATOMIC-RESOLUTION CRYSTAL STRUCTURE OF THE RECOMBINANT FORM OF TITLE 2 SCYTOVIRIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: SCYTOVIRIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: SCYTONEMA VARIUM; SOURCE 3 ORGANISM_TAXID: 423208; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_VECTOR_TYPE: PET32 KEYWDS LECTIN, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR T.MOULAEI,I.BOTOS,N.E.ZIOLKOWSKA,Z.DAUTER,A.WLODAWER REVDAT 6 30-AUG-23 2QSK 1 REMARK REVDAT 5 25-OCT-17 2QSK 1 REMARK REVDAT 4 13-JUL-11 2QSK 1 VERSN REVDAT 3 24-FEB-09 2QSK 1 VERSN REVDAT 2 29-JAN-08 2QSK 1 JRNL REVDAT 1 27-NOV-07 2QSK 0 JRNL AUTH T.MOULAEI,I.BOTOS,N.E.ZIOLKOWSKA,H.R.BOKESCH,L.R.KRUMPE, JRNL AUTH 2 T.C.MCKEE,B.R.O'KEEFE,Z.DAUTER,A.WLODAWER JRNL TITL ATOMIC-RESOLUTION CRYSTAL STRUCTURE OF THE ANTIVIRAL LECTIN JRNL TITL 2 SCYTOVIRIN. JRNL REF PROTEIN SCI. V. 16 2756 2007 JRNL REFN ISSN 0961-8368 JRNL PMID 17965185 JRNL DOI 10.1110/PS.073157507 REMARK 2 REMARK 2 RESOLUTION. 1.00 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 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) : 1.00 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 3 NUMBER OF REFLECTIONS : 47944 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) : 0.129 REMARK 3 R VALUE (WORKING SET) : 0.128 REMARK 3 FREE R VALUE : 0.147 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 2.000 REMARK 3 FREE R VALUE TEST SET COUNT : 980 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) : 1.00 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.03 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2944 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 85.09 REMARK 3 BIN R VALUE (WORKING SET) : 0.2350 REMARK 3 BIN FREE R VALUE SET COUNT : 69 REMARK 3 BIN FREE R VALUE : 0.2600 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 674 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 9 REMARK 3 SOLVENT ATOMS : 129 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 10.18 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.24000 REMARK 3 B22 (A**2) : -0.12000 REMARK 3 B33 (A**2) : -0.13000 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): 0.019 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.020 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.012 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 0.490 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.979 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.972 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 761 ; 0.010 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): 590 ; 0.002 ; 0.020 REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1050 ; 1.392 ; 1.944 REMARK 3 BOND ANGLES OTHERS (DEGREES): 1433 ; 0.885 ; 3.000 REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 117 ; 5.854 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 32 ;33.829 ;24.688 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 113 ;10.879 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 5 ; 6.269 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 99 ; 0.088 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 923 ; 0.010 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): 148 ; 0.001 ; 0.020 REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 172 ; 0.196 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): 614 ; 0.204 ; 0.200 REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 375 ; 0.170 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): 401 ; 0.089 ; 0.200 REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 66 ; 0.260 ; 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): 6 ; 0.132 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): 28 ; 0.255 ; 0.200 REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 10 ; 0.148 ; 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): 659 ; 2.565 ; 2.000 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): 211 ; 1.203 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 817 ; 3.178 ; 3.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 319 ; 3.501 ; 2.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 220 ; 3.687 ; 3.000 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): 1698 ; 1.584 ; 3.000 REMARK 3 SPHERICITY; FREE ATOMS (A**2): 132 ;12.036 ; 3.000 REMARK 3 SPHERICITY; BONDED ATOMS (A**2): 1317 ; 4.858 ; 3.000 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 : NULL 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: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 2QSK COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 09-AUG-07. REMARK 100 THE DEPOSITION ID IS D_1000044001. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-JUL-07 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 22-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.979 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARMOSAIC 300 MM CCD REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 48018 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.000 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : -3.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.8 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 0.05700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.00 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.02 REMARK 200 COMPLETENESS FOR SHELL (%) : 85.3 REMARK 200 DATA REDUNDANCY IN SHELL : 2.20 REMARK 200 R MERGE FOR SHELL (I) : 0.40400 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 1.900 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: SAD/DIRECT REFINEMENT REMARK 200 SOFTWARE USED: SHELXS REMARK 200 STARTING MODEL: PDB ENTRY 2QT4 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 46.02 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.28 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 1M SODIUM CITRATE, 0.1 M IMIDAZOLE PH REMARK 280 8.0, PROTEIN CONCENTRATION 32 MG/ML VAPOR DIFFUSION, HANGING REMARK 280 DROP, TEMPERATURE 293K 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 19.10000 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 29.93500 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 19.39500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 29.93500 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 19.10000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 19.39500 REMARK 290 SMTRY3 4 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: 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 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 OG SER A 82 O HOH A 211 1.84 REMARK 500 O HOH A 211 O HOH A 214 1.91 REMARK 500 O HOH A 165 O HOH A 201 1.97 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 96 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 97 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 98 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC4 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE GOL A 99 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2QT4 RELATED DB: PDB REMARK 900 ATOMIC-RESOLUTION CRYSTAL STRUCTURE OF THE NATURAL FORM OF REMARK 900 SCYTOVIRIN REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE SEQUENCE OF THIS PROTEIN WAS NOT AVAILABLE AT UNP REMARK 999 DATABASE DURING THE TIME OF PROCESSING THIS ENTRY DBREF 2QSK A 1 95 PDB 2QSK 2QSK 1 95 SEQRES 1 A 95 GLY SER GLY PRO THR TYR CYS TRP ASN GLU ALA ASN ASN SEQRES 2 A 95 PRO GLY GLY PRO ASN ARG CYS SER ASN ASN LYS GLN CYS SEQRES 3 A 95 ASP GLY ALA ARG THR CYS SER SER SER GLY PHE CYS GLN SEQRES 4 A 95 GLY THR SER ARG LYS PRO ASP PRO GLY PRO LYS GLY PRO SEQRES 5 A 95 THR TYR CYS TRP ASP GLU ALA LYS ASN PRO GLY GLY PRO SEQRES 6 A 95 ASN ARG CYS SER ASN SER LYS GLN CYS ASP GLY ALA ARG SEQRES 7 A 95 THR CYS SER SER SER GLY PHE CYS GLN GLY THR ALA GLY SEQRES 8 A 95 HIS ALA ALA ALA HET CL A 96 1 HET CL A 97 1 HET CL A 98 1 HET GOL A 99 6 HETNAM CL CHLORIDE ION HETNAM GOL GLYCEROL HETSYN GOL GLYCERIN; PROPANE-1,2,3-TRIOL FORMUL 2 CL 3(CL 1-) FORMUL 5 GOL C3 H8 O3 FORMUL 6 HOH *129(H2 O) HELIX 1 1 ASN A 9 ASN A 13 5 5 HELIX 2 2 ASN A 22 CYS A 26 5 5 HELIX 3 3 ASP A 57 ASN A 61 5 5 HELIX 4 4 ASN A 70 CYS A 74 5 5 SHEET 1 A 2 THR A 31 CYS A 32 0 SHEET 2 A 2 CYS A 38 GLN A 39 -1 O GLN A 39 N THR A 31 SHEET 1 B 2 THR A 79 CYS A 80 0 SHEET 2 B 2 CYS A 86 GLN A 87 -1 O GLN A 87 N THR A 79 SSBOND 1 CYS A 7 CYS A 55 1555 1555 2.04 SSBOND 2 CYS A 20 CYS A 32 1555 1555 2.07 SSBOND 3 CYS A 26 CYS A 38 1555 1555 2.04 SSBOND 4 CYS A 68 CYS A 80 1555 1555 2.07 SSBOND 5 CYS A 74 CYS A 86 1555 1555 2.11 CISPEP 1 LYS A 44 PRO A 45 0 -4.45 CISPEP 2 LYS A 44 PRO A 45 0 -3.62 CISPEP 3 ASP A 46 PRO A 47 0 -2.01 SITE 1 AC1 3 GLY A 15 GLN A 39 ARG A 67 SITE 1 AC2 5 GLY A 3 PRO A 4 THR A 5 HOH A 157 SITE 2 AC2 5 HOH A 160 SITE 1 AC3 1 LYS A 50 SITE 1 AC4 8 GLU A 10 ASN A 18 ASP A 27 SER A 42 SITE 2 AC4 8 ASP A 46 HOH A 126 HOH A 196 HOH A 202 CRYST1 38.200 38.790 59.870 90.00 90.00 90.00 P 21 21 21 4 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 0.026178 0.000000 0.000000 0.00000 SCALE2 0.000000 0.025780 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016703 0.00000