HEADER CALCIUM-BINDING PROTEIN 29-SEP-94 1HML TITLE ALPHA_LACTALBUMIN POSSESSES A DISTINCT ZINC BINDING SITE COMPND MOL_ID: 1; COMPND 2 MOLECULE: ALPHA-LACTALBUMIN; COMPND 3 CHAIN: A; COMPND 4 EC: 2.4.1.22; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS CALCIUM-BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR J.REN,D.I.STUART,K.R.ACHARYA REVDAT 5 20-NOV-24 1HML 1 REMARK REVDAT 4 05-JUN-24 1HML 1 REMARK LINK REVDAT 3 24-FEB-09 1HML 1 VERSN REVDAT 2 01-APR-03 1HML 1 JRNL REVDAT 1 26-JAN-95 1HML 0 JRNL AUTH J.REN,D.I.STUART,K.R.ACHARYA JRNL TITL ALPHA-LACTALBUMIN POSSESSES A DISTINCT ZINC BINDING SITE. JRNL REF J.BIOL.CHEM. V. 268 19292 1993 JRNL REFN ISSN 0021-9258 JRNL PMID 8366079 REMARK 1 REMARK 1 REFERENCE 1 REMARK 1 AUTH K.R.ACHARYA,J.REN,D.I.STUART,D.C.PHILLIPS,R.F.FENNA REMARK 1 TITL CRYSTAL STRUCTURE OF HUMAN ALPHA_LACTALBUMIN AT 7 1.7 REMARK 1 TITL 2 ANGSTROMS RESOLUTION REMARK 1 REF J.MOL.BIOL. V. 221 571 1991 REMARK 1 REFN ISSN 0022-2836 REMARK 1 REFERENCE 2 REMARK 1 AUTH D.I.STUART,K.R.ACHARYA,N.P.C.WALKER,S.G.SMITH,M.LEWIS, REMARK 1 AUTH 2 D.C.PHILLIPS REMARK 1 TITL ALPHA_LACTALBUMIN POSSESSES A NOVEL CALCIUM BINDING LOOP REMARK 1 REF NATURE V. 324 84 1986 REMARK 1 REFN ISSN 0028-0836 REMARK 2 REMARK 2 RESOLUTION. 1.70 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : X-PLOR REMARK 3 AUTHORS : BRUNGER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.70 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 30.00 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : NULL REMARK 3 DATA CUTOFF LOW (ABS(F)) : NULL REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 83.4 REMARK 3 NUMBER OF REFLECTIONS : 10696 REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT. REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : NULL REMARK 3 R VALUE (WORKING SET) : 0.165 REMARK 3 FREE R VALUE : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF FREE R VALUE : NULL REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : NULL REMARK 3 BIN RESOLUTION RANGE HIGH (A) : NULL REMARK 3 BIN RESOLUTION RANGE LOW (A) : NULL REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : NULL REMARK 3 REFLECTIONS IN BIN (WORKING SET) : NULL REMARK 3 BIN R VALUE (WORKING SET) : NULL REMARK 3 BIN FREE R VALUE : NULL REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : NULL REMARK 3 BIN FREE R VALUE TEST SET COUNT : NULL REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : NULL REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 983 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 7 REMARK 3 SOLVENT ATOMS : 112 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : NULL REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.00 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 COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM SIGMAA (A) : NULL REMARK 3 LOW RESOLUTION CUTOFF (A) : NULL REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : NULL REMARK 3 ESD FROM C-V SIGMAA (A) : NULL REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.900 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 23.60 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.500 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : 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 NCS MODEL : NULL REMARK 3 REMARK 3 NCS RESTRAINTS. RMS SIGMA/WEIGHT REMARK 3 GROUP 1 POSITIONAL (A) : NULL ; NULL REMARK 3 GROUP 1 B-FACTOR (A**2) : NULL ; NULL REMARK 3 REMARK 3 PARAMETER FILE 1 : NULL REMARK 3 TOPOLOGY FILE 1 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1HML COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY BNL. REMARK 100 THE DEPOSITION ID IS D_1000173915. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : NULL REMARK 200 PH : NULL REMARK 200 NUMBER OF CRYSTALS USED : NULL REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : NULL REMARK 200 RADIATION SOURCE : NULL REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : NULL REMARK 200 WAVELENGTH OR RANGE (A) : NULL REMARK 200 MONOCHROMATOR : NULL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : NULL REMARK 200 DETECTOR MANUFACTURER : NULL REMARK 200 INTENSITY-INTEGRATION SOFTWARE : NULL REMARK 200 DATA SCALING SOFTWARE : NULL REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 10697 REMARK 200 RESOLUTION RANGE HIGH (A) : NULL REMARK 200 RESOLUTION RANGE LOW (A) : NULL REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 83.4 REMARK 200 DATA REDUNDANCY : NULL REMARK 200 R MERGE (I) : NULL REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : NULL REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : NULL REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : NULL REMARK 200 COMPLETENESS FOR SHELL (%) : NULL REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : NULL REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> FOR SHELL : NULL REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: NULL REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: NULL REMARK 200 SOFTWARE USED: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 30.30 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.76 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: NULL REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 2 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 17.80000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 34.85000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 0.00000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 17.80000 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 34.85000 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: MONOMERIC 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 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 MET A -18 REMARK 465 ARG A -17 REMARK 465 PHE A -16 REMARK 465 PHE A -15 REMARK 465 VAL A -14 REMARK 465 PRO A -13 REMARK 465 LEU A -12 REMARK 465 PHE A -11 REMARK 465 LEU A -10 REMARK 465 VAL A -9 REMARK 465 GLY A -8 REMARK 465 ILE A -7 REMARK 465 LEU A -6 REMARK 465 PHE A -5 REMARK 465 PRO A -4 REMARK 465 ALA A -3 REMARK 465 ILE A -2 REMARK 465 LEU A -1 REMARK 465 ALA A 0 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 ASN A 44 -168.82 -100.97 REMARK 500 ASN A 45 -83.63 -46.55 REMARK 500 LEU A 59 -31.45 -143.70 REMARK 500 ASP A 102 0.63 -67.94 REMARK 500 REMARK 500 REMARK: NULL REMARK 600 REMARK 600 HETEROGEN REMARK 600 REMARK 600 THE MOLECULE ALSO BINDS A SULFATE ION. REMARK 600 REMARK 600 THE ZINC BINDING SITE ALSO INCLUDES RESIDUE GLU 116 FROM A REMARK 600 SYMMETRY-RELATED MOLECULE. REMARK 620 REMARK 620 METAL COORDINATION REMARK 620 (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN IDENTIFIER; REMARK 620 SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 ZN A 125 ZN REMARK 620 N RES CSSEQI ATOM REMARK 620 1 GLU A 49 OE1 REMARK 620 2 GLU A 49 OE2 53.6 REMARK 620 3 GLU A 116 OE1 95.1 147.6 REMARK 620 4 HOH A 146 O 104.4 89.8 108.3 REMARK 620 5 HOH A 147 O 115.8 78.3 114.3 116.4 REMARK 620 N 1 2 3 4 REMARK 620 REMARK 620 COORDINATION ANGLES FOR: M RES CSSEQI METAL REMARK 620 CA A 124 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 79 O REMARK 620 2 ASP A 82 OD1 84.1 REMARK 620 3 ASP A 84 O 170.5 86.4 REMARK 620 4 ASP A 87 OD1 95.6 140.2 91.2 REMARK 620 5 ASP A 88 OD1 98.6 144.3 89.5 75.2 REMARK 620 6 HOH A 140 O 88.9 68.8 87.0 71.4 146.4 REMARK 620 7 HOH A 141 O 90.8 75.0 87.3 144.6 69.4 143.7 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: CA REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: ZN REMARK 800 EVIDENCE_CODE: UNKNOWN REMARK 800 SITE_DESCRIPTION: NULL REMARK 800 REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 124 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE ZN A 125 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE SO4 A 139 DBREF 1HML A -18 123 UNP P00709 LALBA_HUMAN 1 142 SEQRES 1 A 142 MET ARG PHE PHE VAL PRO LEU PHE LEU VAL GLY ILE LEU SEQRES 2 A 142 PHE PRO ALA ILE LEU ALA LYS GLN PHE THR LYS CYS GLU SEQRES 3 A 142 LEU SER GLN LEU LEU LYS ASP ILE ASP GLY TYR GLY GLY SEQRES 4 A 142 ILE ALA LEU PRO GLU LEU ILE CYS THR MET PHE HIS THR SEQRES 5 A 142 SER GLY TYR ASP THR GLN ALA ILE VAL GLU ASN ASN GLU SEQRES 6 A 142 SER THR GLU TYR GLY LEU PHE GLN ILE SER ASN LYS LEU SEQRES 7 A 142 TRP CYS LYS SER SER GLN VAL PRO GLN SER ARG ASN ILE SEQRES 8 A 142 CYS ASP ILE SER CYS ASP LYS PHE LEU ASP ASP ASP ILE SEQRES 9 A 142 THR ASP ASP ILE MET CYS ALA LYS LYS ILE LEU ASP ILE SEQRES 10 A 142 LYS GLY ILE ASP TYR TRP LEU ALA HIS LYS ALA LEU CYS SEQRES 11 A 142 THR GLU LYS LEU GLU GLN TRP LEU CYS GLU LYS LEU HET CA A 124 1 HET ZN A 125 1 HET SO4 A 139 5 HETNAM CA CALCIUM ION HETNAM ZN ZINC ION HETNAM SO4 SULFATE ION FORMUL 2 CA CA 2+ FORMUL 3 ZN ZN 2+ FORMUL 4 SO4 O4 S 2- FORMUL 5 HOH *112(H2 O) HELIX 1 1 THR A 4 LEU A 12 1 9 HELIX 2 2 LYS A 13 ASP A 16 5 4 HELIX 3 3 GLY A 17 ILE A 21 5 5 HELIX 4 4 ALA A 22 GLY A 35 1 14 HELIX 5 5 CYS A 77 LEU A 81 5 5 HELIX 6 6 ILE A 85 LYS A 99 1 15 HELIX 7 7 GLY A 100 TRP A 104 5 5 HELIX 8 8 LEU A 105 CYS A 111 1 7 HELIX 9 9 LEU A 115 LEU A 119 5 5 SHEET 1 A 3 ILE A 41 GLU A 43 0 SHEET 2 A 3 THR A 48 TYR A 50 -1 N GLU A 49 O VAL A 42 SHEET 3 A 3 ILE A 55 SER A 56 -1 N ILE A 55 O TYR A 50 SSBOND 1 CYS A 6 CYS A 120 1555 1555 2.02 SSBOND 2 CYS A 28 CYS A 111 1555 1555 2.03 SSBOND 3 CYS A 61 CYS A 77 1555 1555 2.03 SSBOND 4 CYS A 73 CYS A 91 1555 1555 2.03 LINK OE1 GLU A 49 ZN ZN A 125 1555 1555 2.09 LINK OE2 GLU A 49 ZN ZN A 125 1555 1555 2.66 LINK O LYS A 79 CA CA A 124 1555 1555 2.26 LINK OD1 ASP A 82 CA CA A 124 1555 1555 2.44 LINK O ASP A 84 CA CA A 124 1555 1555 2.28 LINK OD1 ASP A 87 CA CA A 124 1555 1555 2.43 LINK OD1 ASP A 88 CA CA A 124 1555 1555 2.42 LINK OE1 GLU A 116 ZN ZN A 125 4455 1555 2.08 LINK CA CA A 124 O HOH A 140 1555 1555 2.58 LINK CA CA A 124 O HOH A 141 1555 1555 2.57 LINK ZN ZN A 125 O HOH A 146 1555 1555 2.23 LINK ZN ZN A 125 O HOH A 147 1555 1555 2.10 SITE 1 CA 5 LYS A 79 ASP A 82 ASP A 84 ASP A 87 SITE 2 CA 5 ASP A 88 SITE 1 ZN 1 GLU A 49 SITE 1 AC1 7 LYS A 79 ASP A 82 ASP A 84 ASP A 87 SITE 2 AC1 7 ASP A 88 HOH A 140 HOH A 141 SITE 1 AC2 4 GLU A 49 GLU A 116 HOH A 146 HOH A 147 SITE 1 AC3 5 GLN A 39 ARG A 70 LYS A 94 HOH A 154 SITE 2 AC3 5 HOH A 217 CRYST1 35.600 69.700 46.200 90.00 90.00 90.00 P 21 21 2 4 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 0.028090 0.000000 0.000000 0.00000 SCALE2 0.000000 0.014347 0.000000 0.00000 SCALE3 0.000000 0.000000 0.021645 0.00000