HEADER TRANSPORT PROTEIN 30-JAN-99 1B8E TITLE HIGH RESOLUTION CRYSTAL STRUCTURE OF THE BOVINE BETA-LACTOGLOBULIN TITLE 2 (ISOFORMS A AND B) IN ORTHOROMBIC SPACE GROUP COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (BETA-LACTOGLOBULIN); COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: BOS TAURUS; SOURCE 3 ORGANISM_COMMON: CATTLE; SOURCE 4 ORGANISM_TAXID: 9913; SOURCE 5 VARIANT: VARIANT B; SOURCE 6 ORGAN: BREAST; SOURCE 7 TISSUE: MAMMARY GLAND; SOURCE 8 SECRETION: MILK; SOURCE 9 OTHER_DETAILS: ALL REAGENTS WERE PURCHASED FROM SIGMA KEYWDS BETA-LACTOGLOBULIN, VARIANTS, LIPOCALIN, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR K.M.G.OLIVEIRA,L.SAWYER,I.POLIKARPOV REVDAT 5 03-APR-24 1B8E 1 REMARK REVDAT 4 27-DEC-23 1B8E 1 REMARK REVDAT 3 24-FEB-09 1B8E 1 VERSN REVDAT 2 01-APR-03 1B8E 1 JRNL REVDAT 1 02-MAY-01 1B8E 0 JRNL AUTH K.M.OLIVEIRA,V.L.VALENTE-MESQUITA,M.M.BOTELHO,L.SAWYER, JRNL AUTH 2 S.T.FERREIRA,I.POLIKARPOV JRNL TITL CRYSTAL STRUCTURES OF BOVINE BETA-LACTOGLOBULIN IN THE JRNL TITL 2 ORTHORHOMBIC SPACE GROUP C222(1). STRUCTURAL DIFFERENCES JRNL TITL 3 BETWEEN GENETIC VARIANTS A AND B AND FEATURES OF THE TANFORD JRNL TITL 4 TRANSITION. JRNL REF EUR.J.BIOCHEM. V. 268 477 2001 JRNL REFN ISSN 0014-2956 JRNL PMID 11168385 REMARK 2 REMARK 2 RESOLUTION. 1.95 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 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.95 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 9.50 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 85.0 REMARK 3 NUMBER OF REFLECTIONS : 9795 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) : NULL REMARK 3 R VALUE (WORKING SET) : 0.189 REMARK 3 FREE R VALUE : 0.252 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 471 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1197 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 104 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 25.18 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 42.46 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 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.150 REMARK 3 ESU BASED ON FREE R VALUE (A): NULL REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): NULL REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 DISTANCE RESTRAINTS. RMS SIGMA REMARK 3 BOND LENGTH (A) : 0.030 ; NULL REMARK 3 ANGLE DISTANCE (A) : 3.550 ; NULL REMARK 3 INTRAPLANAR 1-4 DISTANCE (A) : NULL ; NULL REMARK 3 H-BOND OR METAL COORDINATION (A) : NULL ; NULL REMARK 3 REMARK 3 PLANE RESTRAINT (A) : NULL ; NULL REMARK 3 CHIRAL-CENTER RESTRAINT (A**3) : NULL ; NULL REMARK 3 REMARK 3 NON-BONDED CONTACT RESTRAINTS. REMARK 3 SINGLE TORSION (A) : NULL ; NULL REMARK 3 MULTIPLE TORSION (A) : NULL ; NULL REMARK 3 H-BOND (X...Y) (A) : NULL ; NULL REMARK 3 H-BOND (X-H...Y) (A) : NULL ; NULL REMARK 3 REMARK 3 CONFORMATIONAL TORSION ANGLE RESTRAINTS. REMARK 3 SPECIFIED (DEGREES) : NULL ; NULL REMARK 3 PLANAR (DEGREES) : NULL ; NULL REMARK 3 STAGGERED (DEGREES) : NULL ; NULL REMARK 3 TRANSVERSE (DEGREES) : NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN BOND (A**2) : NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE (A**2) : NULL ; NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1B8E COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 04-FEB-99. REMARK 100 THE DEPOSITION ID IS D_1000000410. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : SEP-97 REMARK 200 TEMPERATURE (KELVIN) : 291 REMARK 200 PH : 7.9 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : LNLS REMARK 200 BEAMLINE : D03B-MX1 REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.38 REMARK 200 MONOCHROMATOR : SI REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 9834 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.950 REMARK 200 RESOLUTION RANGE LOW (A) : 14.980 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 2.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 86.4 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : 0.08500 REMARK 200 FOR THE DATA SET : 9.2000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.95 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.00 REMARK 200 COMPLETENESS FOR SHELL (%) : 88.8 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : 0.44000 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: AMORE REMARK 200 STARTING MODEL: B-LG LATTICE Y FROM MIXTURE OF GENETIC VARIANTS A REMARK 200 AND B REMARK 200 REMARK 200 REMARK: DATA WERE COLLECTED USING OSCILLATION METHOD REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.00 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.10 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: METHOD IN PRESENCE OF AMMONIUM REMARK 280 SULPHATE 2.5 M, 180MM TRIZMA BUFFER AT A PROTEIN CONCENTRATION REMARK 280 OF 20MG/ML, PH 7.9, VAPOR DIFFUSION, HANGING DROP REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: C 2 2 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,-Y,Z+1/2 REMARK 290 3555 -X,Y,-Z+1/2 REMARK 290 4555 X,-Y,-Z REMARK 290 5555 X+1/2,Y+1/2,Z REMARK 290 6555 -X+1/2,-Y+1/2,Z+1/2 REMARK 290 7555 -X+1/2,Y+1/2,-Z+1/2 REMARK 290 8555 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 33.43000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 0.00000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 33.43000 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 1.000000 0.000000 0.000000 27.82000 REMARK 290 SMTRY2 5 0.000000 1.000000 0.000000 40.82500 REMARK 290 SMTRY3 5 0.000000 0.000000 1.000000 0.00000 REMARK 290 SMTRY1 6 -1.000000 0.000000 0.000000 27.82000 REMARK 290 SMTRY2 6 0.000000 -1.000000 0.000000 40.82500 REMARK 290 SMTRY3 6 0.000000 0.000000 1.000000 33.43000 REMARK 290 SMTRY1 7 -1.000000 0.000000 0.000000 27.82000 REMARK 290 SMTRY2 7 0.000000 1.000000 0.000000 40.82500 REMARK 290 SMTRY3 7 0.000000 0.000000 -1.000000 33.43000 REMARK 290 SMTRY1 8 1.000000 0.000000 0.000000 27.82000 REMARK 290 SMTRY2 8 0.000000 -1.000000 0.000000 40.82500 REMARK 290 SMTRY3 8 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 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 350 BIOMT1 2 -1.000000 0.000000 0.000000 0.00000 REMARK 350 BIOMT2 2 0.000000 1.000000 0.000000 0.00000 REMARK 350 BIOMT3 2 0.000000 0.000000 -1.000000 33.43000 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 PRO A 153 REMARK 465 THR A 154 REMARK 465 GLN A 155 REMARK 465 LEU A 156 REMARK 465 GLU A 157 REMARK 465 GLU A 158 REMARK 465 GLN A 159 REMARK 465 CYS A 160 REMARK 465 HIS A 161 REMARK 465 ILE A 162 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 166 O HOH A 255 2.08 REMARK 500 O HOH A 164 O HOH A 258 2.14 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 ASP A 11 CB - CG - OD2 ANGL. DEV. = -6.0 DEGREES REMARK 500 ARG A 40 NE - CZ - NH2 ANGL. DEV. = -3.6 DEGREES REMARK 500 ASP A 53 CB - CG - OD2 ANGL. DEV. = -5.8 DEGREES REMARK 500 ARG A 124 NE - CZ - NH2 ANGL. DEV. = 3.3 DEGREES REMARK 500 ARG A 148 CD - NE - CZ ANGL. DEV. = 11.8 DEGREES REMARK 500 ARG A 148 NE - CZ - NH1 ANGL. DEV. = 4.1 DEGREES REMARK 500 ARG A 148 NE - CZ - NH2 ANGL. DEV. = -3.5 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 ASP A 33 -81.76 -46.44 REMARK 500 TYR A 99 -38.08 65.49 REMARK 500 LYS A 101 -49.65 -135.21 REMARK 500 PRO A 113 -89.88 -49.58 REMARK 500 GLU A 114 -82.46 -86.05 REMARK 500 GLN A 115 87.51 -154.69 REMARK 500 PRO A 126 24.43 -71.93 REMARK 500 GLU A 127 157.49 -47.38 REMARK 500 VAL A 128 42.64 -93.00 REMARK 500 REMARK 500 REMARK: NULL REMARK 999 REMARK 999 SEQUENCE REMARK 999 THE VARIANT B DIFFERS IN PRIMARY AMINO ACID SEQUENCE FROM REMARK 999 VARIANT A AT THE POSITIONS 64 (GLU-->ASP) AND 118 REMARK 999 (ALA -->VAL) DBREF 1B8E A 1 162 UNP P02754 LACB_BOVIN 17 178 SEQRES 1 A 162 LEU ILE VAL THR GLN THR MET LYS GLY LEU ASP ILE GLN SEQRES 2 A 162 LYS VAL ALA GLY THR TRP TYR SER LEU ALA MET ALA ALA SEQRES 3 A 162 SER ASP ILE SER LEU LEU ASP ALA GLN SER ALA PRO LEU SEQRES 4 A 162 ARG VAL TYR VAL GLU GLU LEU LYS PRO THR PRO GLU GLY SEQRES 5 A 162 ASP LEU GLU ILE LEU LEU GLN LYS TRP GLU ASN GLY GLU SEQRES 6 A 162 CYS ALA GLN LYS LYS ILE ILE ALA GLU LYS THR LYS ILE SEQRES 7 A 162 PRO ALA VAL PHE LYS ILE ASP ALA LEU ASN GLU ASN LYS SEQRES 8 A 162 VAL LEU VAL LEU ASP THR ASP TYR LYS LYS TYR LEU LEU SEQRES 9 A 162 PHE CYS MET GLU ASN SER ALA GLU PRO GLU GLN SER LEU SEQRES 10 A 162 ALA CYS GLN CYS LEU VAL ARG THR PRO GLU VAL ASP ASP SEQRES 11 A 162 GLU ALA LEU GLU LYS PHE ASP LYS ALA LEU LYS ALA LEU SEQRES 12 A 162 PRO MET HIS ILE ARG LEU SER PHE ASN PRO THR GLN LEU SEQRES 13 A 162 GLU GLU GLN CYS HIS ILE FORMUL 2 HOH *104(H2 O) HELIX 1 1 ILE A 2 THR A 6 5 5 HELIX 2 2 ASP A 11 ALA A 16 5 6 HELIX 3 3 ASP A 28 ASP A 33 1 6 HELIX 4 4 ASP A 130 LEU A 140 1 11 HELIX 5 5 LYS A 141 LEU A 143 5 3 SHEET 1 A10 GLY A 17 THR A 18 0 SHEET 2 A10 TYR A 42 PRO A 48 -1 O LEU A 46 N GLY A 17 SHEET 3 A10 LEU A 54 GLU A 62 -1 O GLU A 55 N LYS A 47 SHEET 4 A10 GLU A 65 LYS A 75 -1 O GLU A 65 N GLU A 62 SHEET 5 A10 VAL A 81 ILE A 84 -1 O LYS A 83 N GLU A 74 SHEET 6 A10 ASN A 90 THR A 97 -1 O ASN A 90 N ILE A 84 SHEET 7 A10 TYR A 102 ASN A 109 -1 N LEU A 104 O ASP A 96 SHEET 8 A10 SER A 116 VAL A 123 -1 O SER A 116 N ASN A 109 SHEET 9 A10 TYR A 20 ALA A 26 -1 O TYR A 20 N VAL A 123 SHEET 10 A10 ILE A 147 SER A 150 -1 O ILE A 147 N ALA A 26 SSBOND 1 CYS A 106 CYS A 119 1555 1555 2.06 CRYST1 55.640 81.650 66.860 90.00 90.00 90.00 C 2 2 21 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 0.017973 0.000000 0.000000 0.00000 SCALE2 0.000000 0.012247 0.000000 0.00000 SCALE3 0.000000 0.000000 0.014957 0.00000