HEADER LIGASE 05-APR-21 7EKA TITLE CRYSTAL STRUCTURE OF EPIGALLOCATECHIN BINDING WITH ALPHA-LACTALBUMIN COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-LACTALBUMIN; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: LACTOSE SYNTHASE B PROTEIN; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 GENE: LALBA, ALACTA; SOURCE 6 EXPRESSION_SYSTEM: BOS TAURUS; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 9913 KEYWDS ALPHA-LACTALBUMIN, EPIGALLOCATECHIN; EPIGALLOCATECHIN, LIGASE EXPDTA X-RAY DIFFRACTION AUTHOR J.MA,Q.YAO,X.CHEN,J.ZANG REVDAT 1 08-NOV-23 7EKA 0 JRNL AUTH J.MA,Q.YAO,X.CHEN,C.LV,J.ZANG,G.ZHAO JRNL TITL WEAK BINDING OF EPIGALLOCATECHIN TO ALPHA-LACTALBUMIN JRNL TITL 2 GREATLY IMPROVES ITS STABILITY AND UPTAKE BY CACO-2 CELLS. JRNL REF J.AGRIC.FOOD CHEM. V. 69 8482 2021 JRNL REFN ESSN 1520-5118 JRNL PMID 34286590 JRNL DOI 10.1021/ACS.JAFC.1C03427 REMARK 2 REMARK 2 RESOLUTION. 1.20 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : PHENIX (1.18.2_3874: ???) 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) : 1.20 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 21.21 REMARK 3 MIN(FOBS/SIGMA_FOBS) : 1.370 REMARK 3 COMPLETENESS FOR RANGE (%) : 100.0 REMARK 3 NUMBER OF REFLECTIONS : 50846 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 R VALUE (WORKING + TEST SET) : 0.169 REMARK 3 R VALUE (WORKING SET) : 0.168 REMARK 3 FREE R VALUE : 0.176 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 3.930 REMARK 3 FREE R VALUE TEST SET COUNT : 1999 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 21.2100 - 2.8900 1.00 3572 140 0.1599 0.1570 REMARK 3 2 2.8900 - 2.3000 1.00 3497 144 0.1675 0.1648 REMARK 3 3 2.2900 - 2.0100 1.00 3508 148 0.1602 0.1811 REMARK 3 4 2.0000 - 1.8200 1.00 3479 143 0.1712 0.1800 REMARK 3 5 1.8200 - 1.6900 1.00 3480 141 0.1717 0.1867 REMARK 3 6 1.6900 - 1.5900 1.00 3524 144 0.1671 0.1835 REMARK 3 7 1.5900 - 1.5100 1.00 3465 146 0.1681 0.1710 REMARK 3 8 1.5100 - 1.4500 1.00 3459 148 0.1706 0.1980 REMARK 3 9 1.4500 - 1.3900 1.00 3483 143 0.1756 0.1836 REMARK 3 10 1.3900 - 1.3400 1.00 3476 139 0.1765 0.1863 REMARK 3 11 1.3400 - 1.3000 1.00 3456 141 0.1794 0.2157 REMARK 3 12 1.3000 - 1.2600 1.00 3476 140 0.1837 0.1847 REMARK 3 13 1.2600 - 1.2300 1.00 3497 141 0.1986 0.2281 REMARK 3 14 1.2300 - 1.2000 1.00 3475 141 0.2052 0.2250 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) : 0.100 REMARK 3 PHASE ERROR (DEGREES, MAXIMUM-LIKELIHOOD BASED) : 18.260 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : NULL 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 1019 REMARK 3 ANGLE : 1.848 1383 REMARK 3 CHIRALITY : 0.095 154 REMARK 3 PLANARITY : 0.012 173 REMARK 3 DIHEDRAL : 6.710 125 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 7EKA COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY PDBJ ON 07-APR-21. REMARK 100 THE DEPOSITION ID IS D_1300021622. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 21-MAY-20 REMARK 200 TEMPERATURE (KELVIN) : 90 REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : SSRF REMARK 200 BEAMLINE : BL19U1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 0.9779 REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : PIXEL REMARK 200 DETECTOR MANUFACTURER : PSI JUNGFRAU 16M REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-3000 REMARK 200 DATA SCALING SOFTWARE : HKL-3000 3.27 REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 50847 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.200 REMARK 200 RESOLUTION RANGE LOW (A) : 40.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : NULL REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 94.3 REMARK 200 DATA REDUNDANCY : 9.600 REMARK 200 R MERGE (I) : 0.06700 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 11.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.37 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.40 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.9 REMARK 200 DATA REDUNDANCY IN SHELL : 8.20 REMARK 200 R MERGE FOR SHELL (I) : 0.22000 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: PHENIX REMARK 200 STARTING MODEL: 1ALC REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 58.46 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.96 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 2000 MM AMMONIUM SULFATE, 100 MM REMARK 280 SODIUM CITRATE BUFFER (PH 5.5), EVAPORATION, TEMPERATURE 293K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 64 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -Y,X-Y,Z+1/3 REMARK 290 3555 -X+Y,-X,Z+2/3 REMARK 290 4555 -X,-Y,Z REMARK 290 5555 Y,-X+Y,Z+1/3 REMARK 290 6555 X-Y,X,Z+2/3 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 -0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 2 0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 19.85100 REMARK 290 SMTRY1 3 -0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 3 -0.866025 -0.500000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 1.000000 39.70200 REMARK 290 SMTRY1 4 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 4 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 5 0.500000 0.866025 0.000000 0.00000 REMARK 290 SMTRY2 5 -0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 19.85100 REMARK 290 SMTRY1 6 0.500000 -0.866025 0.000000 0.00000 REMARK 290 SMTRY2 6 0.866025 0.500000 0.000000 0.00000 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 39.70200 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 TOTAL BURIED SURFACE AREA: 260 ANGSTROM**2 REMARK 350 SURFACE AREA OF THE COMPLEX: 6880 ANGSTROM**2 REMARK 350 CHANGE IN SOLVENT FREE ENERGY: -3.0 KCAL/MOL 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 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 302 LIES ON A SPECIAL POSITION. REMARK 470 REMARK 470 MISSING ATOM REMARK 470 THE FOLLOWING RESIDUES HAVE MISSING ATOMS (M=MODEL NUMBER; REMARK 470 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; REMARK 470 I=INSERTION CODE): REMARK 470 M RES CSSEQI ATOMS REMARK 470 GLN A 43 NE2 REMARK 470 ASN A 74 ND2 REMARK 470 ASN A 102 ND2 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 367 O HOH A 462 2.10 REMARK 500 O HOH A 382 O HOH A 449 2.11 REMARK 500 REMARK 500 REMARK: NULL 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 GLN A 43 CB - CA - C ANGL. DEV. = -15.6 DEGREES REMARK 500 GLN A 43 CA - CB - CG ANGL. DEV. = 13.6 DEGREES REMARK 500 ASP A 88 OD1 - CG - OD2 ANGL. DEV. = -34.6 DEGREES REMARK 500 ASP A 88 CB - CG - OD1 ANGL. DEV. = 30.7 DEGREES REMARK 500 ASP A 88 CB - CG - OD2 ANGL. DEV. = -15.5 DEGREES REMARK 500 REMARK 500 REMARK: NULL REMARK 500 REMARK 500 GEOMETRY AND STEREOCHEMISTRY REMARK 500 SUBTOPIC: PLANAR GROUPS REMARK 500 REMARK 500 PLANAR GROUPS IN THE FOLLOWING RESIDUES HAVE A TOTAL REMARK 500 RMS DISTANCE OF ALL ATOMS FROM THE BEST-FIT PLANE REMARK 500 BY MORE THAN AN EXPECTED VALUE OF 6*RMSD, WITH AN REMARK 500 RMSD 0.02 ANGSTROMS, OR AT LEAST ONE ATOM HAS REMARK 500 AN RMSD GREATER THAN THIS VALUE REMARK 500 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 500 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE). REMARK 500 REMARK 500 M RES CSSEQI RMS TYPE REMARK 500 ASP A 88 0.12 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL REMARK 525 REMARK 525 SOLVENT REMARK 525 REMARK 525 THE SOLVENT MOLECULES HAVE CHAIN IDENTIFIERS THAT REMARK 525 INDICATE THE POLYMER CHAIN WITH WHICH THEY ARE MOST REMARK 525 CLOSELY ASSOCIATED. THE REMARK LISTS ALL THE SOLVENT REMARK 525 MOLECULES WHICH ARE MORE THAN 5A AWAY FROM THE REMARK 525 NEAREST POLYMER CHAIN (M = MODEL NUMBER; REMARK 525 RES=RESIDUE NAME; C=CHAIN IDENTIFIER; SSEQ=SEQUENCE REMARK 525 NUMBER; I=INSERTION CODE): REMARK 525 REMARK 525 M RES CSSEQI REMARK 525 HOH A 484 DISTANCE = 5.86 ANGSTROMS REMARK 525 HOH A 485 DISTANCE = 6.61 ANGSTROMS DBREF 7EKA A 1 121 UNP P00711 LALBA_BOVIN 20 140 SEQRES 1 A 121 GLU GLN LEU THR LYS CYS GLU VAL PHE ARG GLU LEU LYS SEQRES 2 A 121 ASP LEU LYS GLY TYR GLY GLY VAL SER LEU PRO GLU TRP SEQRES 3 A 121 VAL CYS THR THR PHE HIS THR SER GLY TYR ASP THR GLN SEQRES 4 A 121 ALA ILE VAL GLN ASN ASN ASP SER THR GLU TYR GLY LEU SEQRES 5 A 121 PHE GLN ILE ASN ASN LYS ILE TRP CYS LYS ASP ASP GLN SEQRES 6 A 121 ASN PRO HIS SER SER ASN ILE CYS ASN ILE SER CYS ASP SEQRES 7 A 121 LYS PHE LEU ASP ASP ASP LEU THR ASP ASP ILE MET CYS SEQRES 8 A 121 VAL LYS LYS ILE LEU ASP LYS VAL GLY ILE ASN TYR TRP SEQRES 9 A 121 LEU ALA HIS LYS ALA LEU CYS SER GLU LYS LEU ASP GLN SEQRES 10 A 121 TRP LEU CYS GLU HET EGT A 201 38 HETNAM EGT 2-(3,4,5-TRIHYDROXY-PHENYL)-CHROMAN-3,5,7-TRIOL HETSYN EGT EPIGALLOCATECHIN FORMUL 2 EGT C15 H14 O7 FORMUL 3 HOH *185(H2 O) HELIX 1 AA1 THR A 4 LEU A 12 1 9 HELIX 2 AA2 LYS A 13 LYS A 16 5 4 HELIX 3 AA3 GLY A 17 VAL A 21 5 5 HELIX 4 AA4 SER A 22 GLY A 35 1 14 HELIX 5 AA5 SER A 76 LEU A 81 5 6 HELIX 6 AA6 LEU A 85 VAL A 99 1 15 HELIX 7 AA7 GLY A 100 TRP A 104 5 5 HELIX 8 AA8 LEU A 105 CYS A 111 1 7 HELIX 9 AA9 LYS A 114 TRP A 118 5 5 SHEET 1 AA1 3 ILE A 41 GLN A 43 0 SHEET 2 AA1 3 THR A 48 TYR A 50 -1 O GLU A 49 N VAL A 42 SHEET 3 AA1 3 ILE A 55 ASN A 56 -1 O ILE A 55 N TYR A 50 SSBOND 1 CYS A 6 CYS A 120 1555 1555 2.01 SSBOND 2 CYS A 28 CYS A 111 1555 1555 2.04 SSBOND 3 CYS A 61 CYS A 77 1555 1555 2.06 SSBOND 4 CYS A 73 CYS A 91 1555 1555 2.06 CRYST1 69.344 69.344 59.553 90.00 90.00 120.00 P 64 6 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 0.014421 0.008326 0.000000 0.00000 SCALE2 0.000000 0.016652 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016792 0.00000