HEADER BIOSYNTHETIC PROTEIN 05-APR-22 7ULR TITLE RECOMBINANT KAPPA-BUNGAROTOXIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: KAPPA-BUNGAROTOXIN; COMPND 3 CHAIN: A, B; COMPND 4 SYNONYM: KAPPA-BGT,KAPPA-1-BUNGAROTOXIN,LONG NEUROTOXIN 2,NEURONAL COMPND 5 BUNGAROTOXIN,NBGT,TOXIN F; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BUNGARUS MULTICINCTUS; SOURCE 3 ORGANISM_COMMON: MANY-BANDED KRAIT; SOURCE 4 ORGANISM_TAXID: 8616; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 6 EXPRESSION_SYSTEM_TAXID: 562 KEYWDS RECOMBINANT, ALPHA NEUROTOXIN, REFOLDED, BIOSYNTHETIC PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.XU,X.LEI,L.CHEN REVDAT 2 25-OCT-23 7ULR 1 REMARK REVDAT 1 03-MAY-23 7ULR 0 JRNL AUTH J.XU,X.LEI,L.CHEN JRNL TITL STRUCTURE OF RECOMBINANT KAPPA-BUNGAROTOXIN AT 1.8 ANGSTROMS JRNL TITL 2 RESOLUTION. JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.80 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.19.2_4158 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 : GEOSTD + MONOMER LIBRARY + CDL V1.2 REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.80 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 36.71 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 2.050 REMARK 3 COMPLETENESS FOR RANGE (%) : 93.4 REMARK 3 NUMBER OF REFLECTIONS : 19602 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.167 REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : 0.190 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.130 REMARK 3 FREE R VALUE TEST SET COUNT : 1006 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 36.7100 - 3.4400 0.97 2774 141 0.1450 0.1965 REMARK 3 2 3.4400 - 2.7300 0.95 2732 150 0.1750 0.1718 REMARK 3 3 2.7300 - 2.3900 0.94 2709 139 0.1782 0.1888 REMARK 3 4 2.3900 - 2.1700 0.93 2639 164 0.1700 0.2112 REMARK 3 5 2.1700 - 2.0100 0.92 2637 136 0.1611 0.1756 REMARK 3 6 2.0100 - 1.8900 0.92 2588 128 0.1656 0.1992 REMARK 3 7 1.8900 - 1.8000 0.90 2517 148 0.1969 0.2006 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) : 0.147 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 20.568 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 20.55 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 : 0.007 1036 REMARK 3 ANGLE : 1.008 1404 REMARK 3 CHIRALITY : 0.056 160 REMARK 3 PLANARITY : 0.010 188 REMARK 3 DIHEDRAL : 16.249 392 REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : 1 REMARK 3 TLS GROUP : 1 REMARK 3 SELECTION: ALL REMARK 3 ORIGIN FOR THE GROUP (A): 0.7935 -3.2321 -10.9890 REMARK 3 T TENSOR REMARK 3 T11: 0.0721 T22: 0.0526 REMARK 3 T33: 0.0358 T12: 0.0003 REMARK 3 T13: 0.0012 T23: 0.0037 REMARK 3 L TENSOR REMARK 3 L11: 0.4891 L22: 0.4192 REMARK 3 L33: 0.3771 L12: 0.2152 REMARK 3 L13: -0.0447 L23: -0.1023 REMARK 3 S TENSOR REMARK 3 S11: -0.0431 S12: 0.0723 S13: 0.0732 REMARK 3 S21: -0.2169 S22: -0.0248 S23: -0.0945 REMARK 3 S31: 0.0818 S32: -0.0121 S33: -0.0039 REMARK 3 REMARK 3 NCS DETAILS REMARK 3 NUMBER OF NCS GROUPS : 1 REMARK 3 NCS GROUP : ens_1 REMARK 3 NCS OPERATOR : 1 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "A" and (resid 2 through 16 or REMARK 3 resid 18 through 30 or resid 32 through REMARK 3 33 or resid 36 through 54 or resid 56 REMARK 3 through 67)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 NCS OPERATOR : 2 REMARK 3 REFERENCE SELECTION: NULL REMARK 3 SELECTION : (chain "B" and (resid 2 through 16 or REMARK 3 resid 18 through 30 or resid 32 through REMARK 3 33 or resid 36 through 54 or resid 56 REMARK 3 through 67)) REMARK 3 ATOM PAIRS NUMBER : NULL REMARK 3 RMSD : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 7ULR COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-APR-22. REMARK 100 THE DEPOSITION ID IS D_1000263681. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 28-MAR-14 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL 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 MICROMAX-007 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.541 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV++ REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MOSFLM REMARK 200 DATA SCALING SOFTWARE : AIMLESS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 19608 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.770 REMARK 200 RESOLUTION RANGE LOW (A) : 36.710 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 93.0 REMARK 200 DATA REDUNDANCY : 4.000 REMARK 200 R MERGE (I) : 0.04700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 13.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.77 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.81 REMARK 200 COMPLETENESS FOR SHELL (%) : 86.3 REMARK 200 DATA REDUNDANCY IN SHELL : 3.90 REMARK 200 R MERGE FOR SHELL (I) : 0.09200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 8.600 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: PHENIX REMARK 200 STARTING MODEL: 1KBA REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 36.80 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.94 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 117 MG/ML IN 200 MM NH4AC, PH 7.0, 1:1 REMARK 280 WITH 0.15 M DL-MALIC ACID PH 7.0, 20% PEG 3350 AT 4 DEGREE REMARK 280 CENTIGRADE, VAPOR DIFFUSION, SITTING DROP, TEMPERATURE 277.15K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,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 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: DIMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: DIMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 1000 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 8060 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -6.0 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 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 172 O HOH A 177 2.07 REMARK 500 OD2 ASP B 20 O HOH B 101 2.09 REMARK 500 OG SER B 9 OG1 THR B 11 2.14 REMARK 500 O HOH B 130 O HOH B 132 2.15 REMARK 500 O HOH B 116 O HOH B 136 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 175 O HOH A 182 1655 1.95 REMARK 500 O HOH B 104 O HOH B 111 1565 2.14 REMARK 500 O HOH A 143 O HOH B 125 1465 2.17 REMARK 500 REMARK 500 REMARK: NULL DBREF 7ULR A 2 67 UNP P01398 3LKB_BUNMU 22 87 DBREF 7ULR B 2 67 UNP P01398 3LKB_BUNMU 22 87 SEQADV 7ULR MET A 1 UNP P01398 INITIATING METHIONINE SEQADV 7ULR MET B 1 UNP P01398 INITIATING METHIONINE SEQRES 1 A 67 MET ARG THR CYS LEU ILE SER PRO SER SER THR PRO GLN SEQRES 2 A 67 THR CYS PRO ASN GLY GLN ASP ILE CYS PHE LEU LYS ALA SEQRES 3 A 67 GLN CYS ASP LYS PHE CYS SER ILE ARG GLY PRO VAL ILE SEQRES 4 A 67 GLU GLN GLY CYS VAL ALA THR CYS PRO GLN PHE ARG SER SEQRES 5 A 67 ASN TYR ARG SER LEU LEU CYS CYS THR THR ASP ASN CYS SEQRES 6 A 67 ASN HIS SEQRES 1 B 67 MET ARG THR CYS LEU ILE SER PRO SER SER THR PRO GLN SEQRES 2 B 67 THR CYS PRO ASN GLY GLN ASP ILE CYS PHE LEU LYS ALA SEQRES 3 B 67 GLN CYS ASP LYS PHE CYS SER ILE ARG GLY PRO VAL ILE SEQRES 4 B 67 GLU GLN GLY CYS VAL ALA THR CYS PRO GLN PHE ARG SER SEQRES 5 B 67 ASN TYR ARG SER LEU LEU CYS CYS THR THR ASP ASN CYS SEQRES 6 B 67 ASN HIS FORMUL 3 HOH *160(H2 O) HELIX 1 AA1 PHE B 31 GLY B 36 1 6 SHEET 1 AA1 2 THR A 3 ILE A 6 0 SHEET 2 AA1 2 THR A 11 THR A 14 -1 O GLN A 13 N CYS A 4 SHEET 1 AA2 6 VAL A 38 VAL A 44 0 SHEET 2 AA2 6 ILE A 21 GLN A 27 -1 N GLN A 27 O VAL A 38 SHEET 3 AA2 6 TYR A 54 CYS A 60 -1 O CYS A 60 N CYS A 22 SHEET 4 AA2 6 TYR B 54 CYS B 60 -1 O LEU B 57 N CYS A 59 SHEET 5 AA2 6 ILE B 21 GLN B 27 -1 N LEU B 24 O LEU B 58 SHEET 6 AA2 6 VAL B 38 VAL B 44 -1 O GLU B 40 N LYS B 25 SHEET 1 AA3 2 THR B 3 ILE B 6 0 SHEET 2 AA3 2 THR B 11 THR B 14 -1 O GLN B 13 N CYS B 4 SSBOND 1 CYS A 4 CYS A 22 1555 1555 2.03 SSBOND 2 CYS A 15 CYS A 43 1555 1555 2.04 SSBOND 3 CYS A 28 CYS A 32 1555 1555 2.06 SSBOND 4 CYS A 47 CYS A 59 1555 1555 2.03 SSBOND 5 CYS A 60 CYS A 65 1555 1555 2.01 SSBOND 6 CYS B 4 CYS B 22 1555 1555 2.04 SSBOND 7 CYS B 15 CYS B 43 1555 1555 2.04 SSBOND 8 CYS B 28 CYS B 32 1555 1555 2.04 SSBOND 9 CYS B 47 CYS B 59 1555 1555 2.05 SSBOND 10 CYS B 60 CYS B 65 1555 1555 2.02 CISPEP 1 SER A 7 PRO A 8 0 2.03 CISPEP 2 SER B 7 PRO B 8 0 1.25 CRYST1 27.090 30.990 39.430 70.44 75.97 71.94 P 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 0.036914 -0.012037 -0.006082 0.00000 SCALE2 0.000000 0.033941 -0.009957 0.00000 SCALE3 0.000000 0.000000 0.027243 0.00000 MTRIX1 1 0.587695 0.666265 0.459027 7.37828 1 MTRIX2 1 0.673120 -0.717416 0.179510 -3.97761 1 MTRIX3 1 0.448915 0.203483 -0.870098 -20.20030 1