HEADER CALCIUM-BINDING PROTEIN 14-FEB-99 1B9O TITLE HUMAN ALPHA-LACTALBUMIN, LOW TEMPERATURE FORM COMPND MOL_ID: 1; COMPND 2 MOLECULE: PROTEIN (ALPHA-LACTALBUMIN); COMPND 3 CHAIN: A SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606 KEYWDS CALCIUM-BINDING PROTEIN, HIGH RESOLUTION EXPDTA X-RAY DIFFRACTION AUTHOR K.HARATA,Y.ABE,M.MURAKI REVDAT 5 30-OCT-24 1B9O 1 REMARK REVDAT 4 27-DEC-23 1B9O 1 REMARK LINK REVDAT 3 04-OCT-17 1B9O 1 REMARK REVDAT 2 24-FEB-09 1B9O 1 VERSN REVDAT 1 31-MAR-99 1B9O 0 JRNL AUTH K.HARATA,Y.ABE,M.MURAKI JRNL TITL CRYSTALLOGRAPHIC EVALUATION OF INTERNAL MOTION OF HUMAN JRNL TITL 2 ALPHA-LACTALBUMIN REFINED BY FULL-MATRIX LEAST-SQUARES JRNL TITL 3 METHOD. JRNL REF J.MOL.BIOL. V. 287 347 1999 JRNL REFN ISSN 0022-2836 JRNL PMID 10080897 JRNL DOI 10.1006/JMBI.1999.2598 REMARK 2 REMARK 2 RESOLUTION. 1.15 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : SHELXL REMARK 3 AUTHORS : G.M.SHELDRICK REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.15 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 23.10 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 98.2 REMARK 3 CROSS-VALIDATION METHOD : NULL REMARK 3 FREE R VALUE TEST SET SELECTION : EVERY 10TH REFLECTION REMARK 3 REMARK 3 FIT TO DATA USED IN REFINEMENT (NO CUTOFF). REMARK 3 R VALUE (WORKING + TEST SET, NO CUTOFF) : 0.119 REMARK 3 R VALUE (WORKING SET, NO CUTOFF) : 0.122 REMARK 3 FREE R VALUE (NO CUTOFF) : 0.162 REMARK 3 FREE R VALUE TEST SET SIZE (%, NO CUTOFF) : 10.000 REMARK 3 FREE R VALUE TEST SET COUNT (NO CUTOFF) : 3769 REMARK 3 TOTAL NUMBER OF REFLECTIONS (NO CUTOFF) : 37696 REMARK 3 REMARK 3 FIT/AGREEMENT OF MODEL FOR DATA WITH F>4SIG(F). REMARK 3 R VALUE (WORKING + TEST SET, F>4SIG(F)) : 0.096 REMARK 3 R VALUE (WORKING SET, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE (F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET SIZE (%, F>4SIG(F)) : NULL REMARK 3 FREE R VALUE TEST SET COUNT (F>4SIG(F)) : NULL REMARK 3 TOTAL NUMBER OF REFLECTIONS (F>4SIG(F)) : 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 : 1 REMARK 3 SOLVENT ATOMS : 164 REMARK 3 REMARK 3 MODEL REFINEMENT. REMARK 3 OCCUPANCY SUM OF NON-HYDROGEN ATOMS : NULL REMARK 3 OCCUPANCY SUM OF HYDROGEN ATOMS : NULL REMARK 3 NUMBER OF DISCRETELY DISORDERED RESIDUES : 11 REMARK 3 NUMBER OF LEAST-SQUARES PARAMETERS : 10757 REMARK 3 NUMBER OF RESTRAINTS : 13066 REMARK 3 REMARK 3 RMS DEVIATIONS FROM RESTRAINT TARGET VALUES. REMARK 3 BOND LENGTHS (A) : 0.014 REMARK 3 ANGLE DISTANCES (A) : 0.014 REMARK 3 SIMILAR DISTANCES (NO TARGET VALUES) (A) : NULL REMARK 3 DISTANCES FROM RESTRAINT PLANES (A) : NULL REMARK 3 ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 NON-ZERO CHIRAL VOLUMES (A**3) : NULL REMARK 3 ANTI-BUMPING DISTANCE RESTRAINTS (A) : 0.100 REMARK 3 RIGID-BOND ADP COMPONENTS (A**2) : 0.016 REMARK 3 SIMILAR ADP COMPONENTS (A**2) : 0.040 REMARK 3 APPROXIMATELY ISOTROPIC ADPS (A**2) : 0.152 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED: MOEWS & KRETSINGER REMARK 3 REMARK 3 STEREOCHEMISTRY TARGET VALUES : NULL REMARK 3 SPECIAL CASE: NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1B9O COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-FEB-99. REMARK 100 THE DEPOSITION ID IS D_1000000485. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : NULL REMARK 200 TEMPERATURE (KELVIN) : 286 REMARK 200 PH : 4.2 REMARK 200 NUMBER OF CRYSTALS USED : 2 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : ENRAF-NONIUS FR571 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.5418 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : ENRAF-NONIUS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : MERGEF, MADNESS REMARK 200 DATA SCALING SOFTWARE : MERGEF REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 37696 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.150 REMARK 200 RESOLUTION RANGE LOW (A) : 23.100 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.0 REMARK 200 DATA REDUNDANCY : 3.500 REMARK 200 R MERGE (I) : 0.05500 REMARK 200 R SYM (I) : NULL REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 10.0000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.15 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.17 REMARK 200 COMPLETENESS FOR SHELL (%) : 96.0 REMARK 200 DATA REDUNDANCY IN SHELL : NULL REMARK 200 R MERGE FOR SHELL (I) : 0.19200 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 <I/SIGMA(I)> 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: X-PLOR REMARK 200 STARTING MODEL: NULL REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 34.31 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 1.87 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PH 4.2 REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 21 21 21 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X+1/2,-Y,Z+1/2 REMARK 290 3555 -X,Y+1/2,-Z+1/2 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 16.59500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 32.10000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 24.77500 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 32.10000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 16.59500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 24.77500 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 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 ARG A 70 0.15 SIDE CHAIN REMARK 500 REMARK 500 REMARK: NULL 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 CA A 124 CA REMARK 620 N RES CSSEQI ATOM REMARK 620 1 LYS A 79 O REMARK 620 2 ASP A 82 OD1 84.0 REMARK 620 3 ASP A 84 O 166.5 83.2 REMARK 620 4 ASP A 87 OD1 95.0 139.1 92.0 REMARK 620 5 ASP A 88 OD1 103.1 143.9 89.8 76.3 REMARK 620 6 HOH A 125 O 89.2 71.0 90.6 149.8 73.7 REMARK 620 7 HOH A 126 O 87.6 70.0 84.1 69.1 144.6 141.0 REMARK 620 N 1 2 3 4 5 6 REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CA A 124 DBREF 1B9O A 1 123 UNP P00709 LALBA_HUMAN 1 123 SEQRES 1 A 123 LYS GLN PHE THR LYS CYS GLU LEU SER GLN LEU LEU LYS SEQRES 2 A 123 ASP ILE ASP GLY TYR GLY GLY ILE ALA LEU PRO GLU LEU SEQRES 3 A 123 ILE CYS THR MET PHE HIS THR SER GLY TYR ASP THR GLN SEQRES 4 A 123 ALA ILE VAL GLU ASN ASP GLU SER THR GLU TYR GLY LEU SEQRES 5 A 123 PHE GLN ILE SER ASN LYS LEU TRP CYS LYS SER SER GLN SEQRES 6 A 123 VAL PRO GLN SER ARG ASN ILE CYS ASP ILE SER CYS ASP SEQRES 7 A 123 LYS PHE LEU ASP ASP ASP ILE THR ASP ASP ILE MET CYS SEQRES 8 A 123 ALA LYS LYS ILE LEU ASP ILE LYS GLY ILE ASP TYR TRP SEQRES 9 A 123 LEU ALA HIS LYS ALA LEU CYS THR GLU LYS LEU GLU GLN SEQRES 10 A 123 TRP LEU CYS GLU LYS LEU HET CA A 124 1 HETNAM CA CALCIUM ION FORMUL 2 CA CA 2+ FORMUL 3 HOH *164(H2 O) HELIX 1 1 LYS A 5 LEU A 11 1 7 HELIX 2 2 LYS A 13 ILE A 15 5 3 HELIX 3 3 TYR A 18 GLY A 20 5 3 HELIX 4 4 LEU A 23 SER A 34 1 12 HELIX 5 5 CYS A 77 LEU A 81 5 5 HELIX 6 6 THR A 86 ILE A 98 1 13 HELIX 7 7 GLY A 100 LEU A 105 5 6 HELIX 8 8 LEU A 115 TRP A 118 5 4 SHEET 1 A 2 ILE A 41 GLU A 43 0 SHEET 2 A 2 THR A 48 TYR A 50 -1 N GLU A 49 O VAL A 42 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 2.01 SSBOND 4 CYS A 73 CYS A 91 1555 1555 2.03 LINK O LYS A 79 CA CA A 124 1555 1555 2.26 LINK OD1 ASP A 82 CA CA A 124 1555 1555 2.38 LINK O ASP A 84 CA CA A 124 1555 1555 2.24 LINK OD1 ASP A 87 CA CA A 124 1555 1555 2.41 LINK OD1 ASP A 88 CA CA A 124 1555 1555 2.37 LINK CA CA A 124 O HOH A 125 1555 1555 2.42 LINK CA CA A 124 O HOH A 126 1555 1555 2.49 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 125 HOH A 126 CRYST1 33.190 49.550 64.200 90.00 90.00 90.00 P 21 21 21 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 0.030129 0.000000 0.000000 0.00000 SCALE2 0.000000 0.020182 0.000000 0.00000 SCALE3 0.000000 0.000000 0.015576 0.00000