HEADER SUGAR BINDING PROTEIN 01-JUN-09 3HNU TITLE CRYSTAL STRUCTURE OF A DESIGNED CYANOVIRIN-N HOMOLOG LECTIN; LKAMG IN TITLE 2 P21 SPACE GROUP COMPND MOL_ID: 1; COMPND 2 MOLECULE: CYANOVIRIN-N-LIKE PROTEIN; COMPND 3 CHAIN: X; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: TUBER BORCHII, NEUROSPORA CRASSA; SOURCE 3 ORGANISM_TAXID: 42251, 5141; SOURCE 4 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 5 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 6 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 8 EXPRESSION_SYSTEM_PLASMID: PET15B KEYWDS CYANOVIRIN-N, CVNH, LECTIN, SUGAR BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR L.M.I.KOHARUDIN,W.FUREY,A.M.GRONENBORN REVDAT 4 06-SEP-23 3HNU 1 SEQADV REVDAT 3 16-AUG-17 3HNU 1 SOURCE AUTHOR REMARK REVDAT 2 03-NOV-09 3HNU 1 JRNL REVDAT 1 23-JUN-09 3HNU 0 JRNL AUTH L.M.KOHARUDIN,W.FUREY,A.M.GRONENBORN JRNL TITL A DESIGNED CHIMERIC CYANOVIRIN-N HOMOLOG LECTIN: STRUCTURE JRNL TITL 2 AND MOLECULAR BASIS OF SUCROSE BINDING. JRNL REF PROTEINS V. 77 904 2009 JRNL REFN ISSN 0887-3585 JRNL PMID 19639634 JRNL DOI 10.1002/PROT.22514 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH L.M.KOHARUDIN,A.R.VISCOMI,J.G.JEE,S.OTTONELLO,A.M.GRONENBORN REMARK 1 TITL THE EVOLUTIONARILY CONSERVED FAMILY OF CYANOVIRIN-N REMARK 1 TITL 2 HOMOLOGS: STRUCTURES AND CARBOHYDRATE SPECIFICITY REMARK 1 REF STRUCTURE V. 16 570 2008 REMARK 1 REFN ISSN 0969-2126 REMARK 1 PMID 18400178 REMARK 2 REMARK 2 RESOLUTION. 1.56 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.5.0044 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) : 1.56 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 24.49 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 3 NUMBER OF REFLECTIONS : 12776 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) : 0.183 REMARK 3 FREE R VALUE : 0.225 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.100 REMARK 3 FREE R VALUE TEST SET COUNT : 1436 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) : 1.56 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.60 REMARK 3 REFLECTION IN BIN (WORKING SET) : 644 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 65.83 REMARK 3 BIN R VALUE (WORKING SET) : 0.3390 REMARK 3 BIN FREE R VALUE SET COUNT : 67 REMARK 3 BIN FREE R VALUE : 0.3820 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 841 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 167 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 17.88 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.53000 REMARK 3 B22 (A**2) : -0.18000 REMARK 3 B33 (A**2) : 0.65000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.14000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.104 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.105 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.057 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.542 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.963 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.938 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 881 ; 0.009 ; 0.021 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 1197 ; 1.141 ; 1.912 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 111 ; 7.624 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 55 ;29.281 ;24.000 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 140 ;11.102 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 11 ;21.919 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 125 ; 0.098 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 724 ; 0.013 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL 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): 540 ; 1.375 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 866 ; 2.311 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 341 ; 3.696 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 331 ; 5.965 ; 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 : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.40 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 3HNU COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 05-JUN-09. REMARK 100 THE DEPOSITION ID IS D_1000053363. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 16-OCT-06 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 8.0 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 FR-E SUPERBRIGHT REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : OSMIC MIRRORS REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : RIGAKU SATURN 944 REMARK 200 INTENSITY-INTEGRATION SOFTWARE : D*TREK REMARK 200 DATA SCALING SOFTWARE : D*TREK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14212 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.560 REMARK 200 RESOLUTION RANGE LOW (A) : 24.490 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.5 REMARK 200 DATA REDUNDANCY : 3.900 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 19.9000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.56 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.62 REMARK 200 COMPLETENESS FOR SHELL (%) : 71.4 REMARK 200 DATA REDUNDANCY IN SHELL : 2.21 REMARK 200 R MERGE FOR SHELL (I) : 0.17500 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 3.200 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: PSEUDO-MONOMERIC CV-N (1M5M) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.65 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.11 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 40 MG/ML PROTEIN IN 0.2 M LI2SO4, 0.1 REMARK 280 M TRIS-HCL (PH 8.5), AND 30% PEG 4000 AT 8 TO 1 RATIO BETWEEN REMARK 280 PROTEIN AND MOTHER LIQUOR, VAPOR DIFFUSION, SITTING DROP, REMARK 280 TEMPERATURE 277K, PH 8.0 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 17.22200 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: MONOMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 APPLY THE FOLLOWING TO CHAINS: X 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 GLY X -2 REMARK 465 SER X -1 REMARK 465 HIS X 0 REMARK 465 GLN X 107 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 SER X 6 26.34 -142.26 REMARK 500 LYS X 67 56.37 -145.24 REMARK 500 REMARK 500 REMARK: NULL REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 2KJL RELATED DB: PDB REMARK 900 SOLUTION STRUCTURES OF A DESIGNED CYANOVIRIN-N HOMOLOG LECTIN; LKAMG REMARK 900 RELATED ID: 3HNX RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A DESIGNED CYANOVIRIN-N HOMOLOG LECTIN; LKAMG REMARK 900 IN P212121 SPACE GROUP REMARK 900 RELATED ID: 3HP8 RELATED DB: PDB REMARK 900 CRYSTAL STRUCTURE OF A DESIGNED CYANOVIRIN-N HOMOLOG LECTIN; LKAMG, REMARK 900 BOUND TO SUCROSE DBREF 3HNU X 1 39 UNP Q5MK11 Q5MK11_TUBBO 1 39 DBREF 3HNU X 40 93 UNP Q7S6U4 Q7S6U4_NEUCR 42 95 DBREF 3HNU X 94 107 UNP Q5MK11 Q5MK11_TUBBO 90 103 SEQADV 3HNU GLY X -2 UNP Q5MK11 EXPRESSION TAG SEQADV 3HNU SER X -1 UNP Q5MK11 EXPRESSION TAG SEQADV 3HNU HIS X 0 UNP Q5MK11 EXPRESSION TAG SEQRES 1 X 110 GLY SER HIS MET SER TYR ALA ASP SER SER ARG ASN ALA SEQRES 2 X 110 VAL LEU THR ASN GLY GLY ARG THR LEU ARG ALA GLU CYS SEQRES 3 X 110 ARG ASN ALA ASP GLY ASN TRP VAL THR SER GLU LEU ASP SEQRES 4 X 110 LEU ASP THR ILE ILE GLY ASN ASN ASP GLY HIS PHE GLN SEQRES 5 X 110 TRP GLY GLY GLN ASN PHE THR GLU THR ALA GLU ASP ILE SEQRES 6 X 110 ARG PHE HIS PRO LYS GLU GLY ALA ALA GLU GLN PRO ILE SEQRES 7 X 110 LEU ARG ALA ARG LEU ARG ASP CYS ASN GLY GLU PHE HIS SEQRES 8 X 110 ASP ARG ASP VAL ASN LEU ASN ARG ILE GLN ASN VAL ASN SEQRES 9 X 110 GLY ARG LEU VAL PHE GLN FORMUL 2 HOH *167(H2 O) HELIX 1 1 SER X 2 ASP X 5 5 4 HELIX 2 2 ASN X 54 GLU X 57 5 4 HELIX 3 3 ASN X 95 ILE X 97 5 3 SHEET 1 A 3 SER X 7 THR X 13 0 SHEET 2 A 3 THR X 18 ARG X 24 -1 O THR X 18 N THR X 13 SHEET 3 A 3 TRP X 30 ASP X 36 -1 O VAL X 31 N CYS X 23 SHEET 1 B 2 ILE X 41 ASN X 44 0 SHEET 2 B 2 HIS X 47 TRP X 50 -1 O HIS X 47 N ASN X 44 SHEET 1 C 3 ALA X 59 GLU X 68 0 SHEET 2 C 3 GLN X 73 ARG X 81 -1 O ARG X 79 N GLU X 60 SHEET 3 C 3 PHE X 87 ASN X 93 -1 O ARG X 90 N ALA X 78 SHEET 1 D 2 GLN X 98 VAL X 100 0 SHEET 2 D 2 ARG X 103 VAL X 105 -1 O VAL X 105 N GLN X 98 CRYST1 33.876 34.444 45.632 90.00 101.24 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 0.029519 0.000000 0.005866 0.00000 SCALE2 0.000000 0.029033 0.000000 0.00000 SCALE3 0.000000 0.000000 0.022343 0.00000