HEADER ANTIMICROBIAL PROTEIN 13-JUL-21 7P4Z TITLE CRYSTAL STRUCTURE OF AVIDIN FROM HEN EGG WHITE IN SPACE GROUP C2 COMPND MOL_ID: 1; COMPND 2 MOLECULE: AVIDIN; COMPND 3 CHAIN: A, B SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: GALLUS GALLUS; SOURCE 3 ORGANISM_COMMON: CHICKEN; SOURCE 4 ORGANISM_TAXID: 9031 KEYWDS AVIDIN, GALLUS, ANTIMICROBIAL PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR D.BELLINI,F.GORREC REVDAT 3 31-JAN-24 7P4Z 1 REMARK REVDAT 2 11-MAY-22 7P4Z 1 JRNL REVDAT 1 25-AUG-21 7P4Z 0 JRNL AUTH F.GORREC,D.BELLINI JRNL TITL THE FUSION PROTEIN CRYSTALLIZATION SCREEN. JRNL REF J.APPL.CRYSTALLOGR. V. 55 310 2022 JRNL REFN ISSN 0021-8898 JRNL PMID 35497656 JRNL DOI 10.1107/S1600576722001765 REMARK 2 REMARK 2 RESOLUTION. 2.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX 1.17.1_3660 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) : 2.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 58.90 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.400 REMARK 3 COMPLETENESS FOR RANGE (%) : 99.2 REMARK 3 NUMBER OF REFLECTIONS : 14835 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.249 REMARK 3 R VALUE (WORKING SET) : 0.247 REMARK 3 FREE R VALUE : 0.291 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.320 REMARK 3 FREE R VALUE TEST SET COUNT : 789 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 58.9000 - 4.0000 1.00 2420 135 0.2195 0.2531 REMARK 3 2 3.9900 - 3.1700 1.00 2354 141 0.2397 0.3049 REMARK 3 3 3.1700 - 2.7700 1.00 2354 125 0.2655 0.2817 REMARK 3 4 2.7700 - 2.5200 0.99 2318 145 0.2782 0.3399 REMARK 3 5 2.5200 - 2.3400 0.99 2322 119 0.2896 0.3663 REMARK 3 6 2.3400 - 2.2000 0.97 2278 124 0.2922 0.3137 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) : 0.257 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 36.350 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 34.57 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 49.63 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 : 0.008 1891 REMARK 3 ANGLE : 1.213 2555 REMARK 3 CHIRALITY : 0.131 297 REMARK 3 PLANARITY : 0.010 317 REMARK 3 DIHEDRAL : 6.970 254 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 7P4Z COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBE ON 13-JUL-21. REMARK 100 THE DEPOSITION ID IS D_1292117021. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 02-JUL-21 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : DIAMOND REMARK 200 BEAMLINE : I04 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9795 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : DECTRIS EIGER2 XE 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DIALS REMARK 200 DATA SCALING SOFTWARE : DIALS REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 14917 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.200 REMARK 200 RESOLUTION RANGE LOW (A) : 58.920 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 99.8 REMARK 200 DATA REDUNDANCY : 4.600 REMARK 200 R MERGE (I) : 6.00000 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 15.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.20 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.24 REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 9.90000 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 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: MOLREP REMARK 200 STARTING MODEL: 1Y53 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 56.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.80 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 10% W/V PEG 8000, 20% V/V ETHYLENE REMARK 280 GLYCOL, 0.1 M MES/IMIDAZOLE PH 6.5, 0.4% OF EACH ANAESTHETIC REMARK 280 ALKALOID (MORPHEUS FUSION SCREEN, WELL H12), VAPOR DIFFUSION, REMARK 280 SITTING DROP, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 1 2 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,Y,-Z REMARK 290 3555 X+1/2,Y+1/2,Z 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 0.00000 REMARK 290 SMTRY2 2 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 3 1.000000 0.000000 0.000000 57.21200 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.65200 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 57.21200 REMARK 290 SMTRY2 4 0.000000 1.000000 0.000000 21.65200 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: TETRAMERIC REMARK 350 SOFTWARE DETERMINED QUATERNARY STRUCTURE: TETRAMERIC REMARK 350 SOFTWARE USED: PISA REMARK 350 TOTAL BURIED SURFACE AREA: 11120 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 20360 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -31.0 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 -20.33269 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 58.90345 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 301 LIES ON A SPECIAL POSITION. 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 THR A 62 REMARK 465 ALA A 63 REMARK 465 THR A 64 REMARK 465 SER A 65 REMARK 465 ASN A 66 REMARK 465 VAL B 61 REMARK 465 THR B 62 REMARK 465 ALA B 63 REMARK 465 THR B 64 REMARK 465 SER B 65 REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: COVALENT BOND ANGLES REMARK 500 REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 STANDARD TABLE: REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1) REMARK 500 REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999 REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996 REMARK 500 REMARK 500 M RES CSSEQI ATM1 ATM2 ATM3 REMARK 500 PHE B 88 CB - CG - CD2 ANGL. DEV. = -4.4 DEGREES REMARK 500 PHE B 88 CB - CG - CD1 ANGL. DEV. = 4.7 DEGREES REMARK 500 PHE B 90 CB - CG - CD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 PHE B 90 CB - CG - CD1 ANGL. DEV. = 4.8 DEGREES REMARK 500 REMARK 500 REMARK: NULL 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 LYS B 82 58.70 39.92 REMARK 500 PHE B 90 142.98 -170.52 REMARK 500 ASP B 110 -169.19 -72.22 REMARK 500 REMARK 500 REMARK: NULL DBREF 7P4Z A 27 147 UNP P02701 AVID_CHICK 27 147 DBREF 7P4Z B 27 147 UNP P02701 AVID_CHICK 27 147 SEQRES 1 A 121 LYS CYS SER LEU THR GLY LYS TRP THR ASN ASP LEU GLY SEQRES 2 A 121 SER ASN MET THR ILE GLY ALA VAL ASN SER ARG GLY GLU SEQRES 3 A 121 PHE THR GLY THR TYR ILE THR ALA VAL THR ALA THR SER SEQRES 4 A 121 ASN GLU ILE LYS GLU SER PRO LEU HIS GLY THR GLN ASN SEQRES 5 A 121 THR ILE ASN LYS ARG THR GLN PRO THR PHE GLY PHE THR SEQRES 6 A 121 VAL ASN TRP LYS PHE SER GLU SER THR THR VAL PHE THR SEQRES 7 A 121 GLY GLN CYS PHE ILE ASP ARG ASN GLY LYS GLU VAL LEU SEQRES 8 A 121 LYS THR MET TRP LEU LEU ARG SER SER VAL ASN ASP ILE SEQRES 9 A 121 GLY ASP ASP TRP LYS ALA THR ARG VAL GLY ILE ASN ILE SEQRES 10 A 121 PHE THR ARG LEU SEQRES 1 B 121 LYS CYS SER LEU THR GLY LYS TRP THR ASN ASP LEU GLY SEQRES 2 B 121 SER ASN MET THR ILE GLY ALA VAL ASN SER ARG GLY GLU SEQRES 3 B 121 PHE THR GLY THR TYR ILE THR ALA VAL THR ALA THR SER SEQRES 4 B 121 ASN GLU ILE LYS GLU SER PRO LEU HIS GLY THR GLN ASN SEQRES 5 B 121 THR ILE ASN LYS ARG THR GLN PRO THR PHE GLY PHE THR SEQRES 6 B 121 VAL ASN TRP LYS PHE SER GLU SER THR THR VAL PHE THR SEQRES 7 B 121 GLY GLN CYS PHE ILE ASP ARG ASN GLY LYS GLU VAL LEU SEQRES 8 B 121 LYS THR MET TRP LEU LEU ARG SER SER VAL ASN ASP ILE SEQRES 9 B 121 GLY ASP ASP TRP LYS ALA THR ARG VAL GLY ILE ASN ILE SEQRES 10 B 121 PHE THR ARG LEU HET NAG A 201 14 HET NAG B 201 14 HETNAM NAG 2-ACETAMIDO-2-DEOXY-BETA-D-GLUCOPYRANOSE 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 FORMUL 3 NAG 2(C8 H15 N O6) FORMUL 5 HOH *13(H2 O) HELIX 1 AA1 THR A 79 ARG A 83 5 5 HELIX 2 AA2 ASP A 129 LYS A 135 5 7 HELIX 3 AA3 THR B 79 ARG B 83 5 5 HELIX 4 AA4 ASP B 129 LYS B 135 5 7 SHEET 1 AA1 9 GLY A 32 ASN A 36 0 SHEET 2 AA1 9 ASN A 41 ILE A 44 -1 O MET A 42 N TRP A 34 SHEET 3 AA1 9 GLU A 52 THR A 59 -1 O ILE A 58 N ASN A 41 SHEET 4 AA1 9 LYS A 69 GLN A 77 -1 O SER A 71 N TYR A 57 SHEET 5 AA1 9 THR A 87 VAL A 92 -1 O THR A 91 N HIS A 74 SHEET 6 AA1 9 THR A 100 ILE A 109 -1 O THR A 101 N VAL A 92 SHEET 7 AA1 9 GLU A 115 ARG A 124 -1 O ARG A 124 N THR A 100 SHEET 8 AA1 9 THR A 137 ARG A 146 -1 O ARG A 138 N LEU A 123 SHEET 9 AA1 9 GLY A 32 ASN A 36 -1 N THR A 35 O THR A 145 SHEET 1 AA2 9 GLY B 32 ASN B 36 0 SHEET 2 AA2 9 ASN B 41 ILE B 44 -1 O MET B 42 N TRP B 34 SHEET 3 AA2 9 GLU B 52 THR B 59 -1 O ILE B 58 N ASN B 41 SHEET 4 AA2 9 LYS B 69 GLN B 77 -1 O SER B 71 N TYR B 57 SHEET 5 AA2 9 THR B 87 VAL B 92 -1 O THR B 91 N HIS B 74 SHEET 6 AA2 9 THR B 100 ILE B 109 -1 O THR B 101 N VAL B 92 SHEET 7 AA2 9 GLU B 115 ARG B 124 -1 O ARG B 124 N THR B 100 SHEET 8 AA2 9 THR B 137 ARG B 146 -1 O PHE B 144 N LEU B 117 SHEET 9 AA2 9 GLY B 32 ASN B 36 -1 N THR B 35 O THR B 145 SSBOND 1 CYS A 28 CYS A 107 1555 1555 2.03 SSBOND 2 CYS B 28 CYS B 107 1555 1555 2.02 LINK ND2 ASN A 41 C1 NAG A 201 1555 1555 1.44 LINK ND2 ASN B 41 C1 NAG B 201 1555 1555 1.44 CRYST1 114.424 43.304 62.314 90.00 109.04 90.00 C 1 2 1 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 0.008739 0.000000 0.003017 0.00000 SCALE2 0.000000 0.023093 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016977 0.00000