HEADER LIPID BINDING PROTEIN 24-JUN-03 1PUB TITLE GM2-ACTIVATOR PROTEIN CRYSTAL STRUCTURE COMPND MOL_ID: 1; COMPND 2 MOLECULE: GM2-ACTIVATOR PROTEIN; COMPND 3 CHAIN: A; COMPND 4 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 6 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 7 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 8 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 9 EXPRESSION_SYSTEM_PLASMID: PT513 KEYWDS BETA-CUP, ENLARGE LIPID BINDING POCKET, LIPID BINDING PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR C.S.WRIGHT,Q.ZHAO,F.RASTINEJAD REVDAT 5 20-NOV-24 1PUB 1 REMARK REVDAT 4 16-AUG-23 1PUB 1 REMARK REVDAT 3 01-SEP-09 1PUB 1 REMARK HETATM HETNAM REVDAT 2 24-FEB-09 1PUB 1 VERSN REVDAT 1 29-JUN-04 1PUB 0 JRNL AUTH C.S.WRIGHT,Q.ZHAO,F.RASTINEJAD JRNL TITL STRUCTURAL ANALYSIS OF LIPID COMPLEXES OF GM2-ACTIVATOR JRNL TITL 2 PROTEIN. JRNL REF J.MOL.BIOL. V. 331 951 2003 JRNL REFN ISSN 0022-2836 JRNL PMID 12909021 JRNL DOI 10.1016/S0022-2836(03)00794-0 REMARK 2 REMARK 2 RESOLUTION. 2.51 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : CNS 1.0 REMARK 3 AUTHORS : BRUNGER,ADAMS,CLORE,DELANO,GROS,GROSSE- REMARK 3 : KUNSTLEVE,JIANG,KUSZEWSKI,NILGES,PANNU, REMARK 3 : READ,RICE,SIMONSON,WARREN REMARK 3 REMARK 3 REFINEMENT TARGET : ENGH & HUBER REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 2.51 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 7.99 REMARK 3 DATA CUTOFF (SIGMA(F)) : 1.000 REMARK 3 DATA CUTOFF HIGH (ABS(F)) : 968320.300 REMARK 3 DATA CUTOFF LOW (ABS(F)) : 0.0000 REMARK 3 COMPLETENESS (WORKING+TEST) (%) : 98.1 REMARK 3 NUMBER OF REFLECTIONS : 6640 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 SET) : 0.209 REMARK 3 FREE R VALUE : 0.286 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 10.900 REMARK 3 FREE R VALUE TEST SET COUNT : 727 REMARK 3 ESTIMATED ERROR OF FREE R VALUE : 0.011 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 6 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 2.51 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 2.65 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 84.30 REMARK 3 REFLECTIONS IN BIN (WORKING SET) : 849 REMARK 3 BIN R VALUE (WORKING SET) : 0.3560 REMARK 3 BIN FREE R VALUE : 0.4030 REMARK 3 BIN FREE R VALUE TEST SET SIZE (%) : 10.70 REMARK 3 BIN FREE R VALUE TEST SET COUNT : 102 REMARK 3 ESTIMATED ERROR OF BIN FREE R VALUE : 0.040 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1232 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 48 REMARK 3 SOLVENT ATOMS : 61 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 56.40 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 50.40 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 7.18000 REMARK 3 B22 (A**2) : -6.86000 REMARK 3 B33 (A**2) : -0.32000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : 0.00000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM LUZZATI PLOT (A) : 0.31 REMARK 3 ESD FROM SIGMAA (A) : 0.50 REMARK 3 LOW RESOLUTION CUTOFF (A) : 5.00 REMARK 3 REMARK 3 CROSS-VALIDATED ESTIMATED COORDINATE ERROR. REMARK 3 ESD FROM C-V LUZZATI PLOT (A) : 0.46 REMARK 3 ESD FROM C-V SIGMAA (A) : 0.60 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES. REMARK 3 BOND LENGTHS (A) : 0.010 REMARK 3 BOND ANGLES (DEGREES) : 1.500 REMARK 3 DIHEDRAL ANGLES (DEGREES) : 25.90 REMARK 3 IMPROPER ANGLES (DEGREES) : 1.020 REMARK 3 REMARK 3 ISOTROPIC THERMAL MODEL : RESTRAINED REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. RMS SIGMA REMARK 3 MAIN-CHAIN BOND (A**2) : 3.910 ; 1.500 REMARK 3 MAIN-CHAIN ANGLE (A**2) : 5.810 ; 2.000 REMARK 3 SIDE-CHAIN BOND (A**2) : 10.980; 2.000 REMARK 3 SIDE-CHAIN ANGLE (A**2) : 10.350; 2.500 REMARK 3 REMARK 3 BULK SOLVENT MODELING. REMARK 3 METHOD USED : FLAT MODEL REMARK 3 KSOL : 0.39 REMARK 3 BSOL : 102.3 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 : PROTEIN_REP.PARAM REMARK 3 PARAMETER FILE 2 : PA_XPLOR.PARAM REMARK 3 PARAMETER FILE 3 : SOLVENT_REP.PARAM REMARK 3 PARAMETER FILE 4 : NULL REMARK 3 TOPOLOGY FILE 1 : PROTEIN.TOP REMARK 3 TOPOLOGY FILE 2 : PA_XPLOR.TOP REMARK 3 TOPOLOGY FILE 3 : SOLVENT.TOP REMARK 3 TOPOLOGY FILE 4 : NULL REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: NULL REMARK 4 REMARK 4 1PUB COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 27-JUN-03. REMARK 100 THE DEPOSITION ID IS D_1000019573. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 20-FEB-95 REMARK 200 TEMPERATURE (KELVIN) : 298.0 REMARK 200 PH : 5.6 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : N REMARK 200 RADIATION SOURCE : ROTATING ANODE REMARK 200 BEAMLINE : NULL REMARK 200 X-RAY GENERATOR MODEL : RIGAKU REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54041 REMARK 200 MONOCHROMATOR : GRAPHITE REMARK 200 OPTICS : MIRRORS REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 7091 REMARK 200 RESOLUTION RANGE HIGH (A) : 2.500 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 98.6 REMARK 200 DATA REDUNDANCY : 3.000 REMARK 200 R MERGE (I) : 0.12800 REMARK 200 R SYM (I) : 0.12800 REMARK 200 <I/SIGMA(I)> FOR THE DATA SET : 3.5000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 2.50 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 2.59 REMARK 200 COMPLETENESS FOR SHELL (%) : 98.7 REMARK 200 DATA REDUNDANCY IN SHELL : 3.00 REMARK 200 R MERGE FOR SHELL (I) : 0.75100 REMARK 200 R SYM FOR SHELL (I) : 0.75000 REMARK 200 <I/SIGMA(I)> FOR SHELL : 1.300 REMARK 200 REMARK 200 DIFFRACTION PROTOCOL: SINGLE WAVELENGTH REMARK 200 METHOD USED TO DETERMINE THE STRUCTURE: MOLECULAR REPLACEMENT REMARK 200 SOFTWARE USED: CNS REMARK 200 STARTING MODEL: MONOMER A OF PDB ENTRY 1G13 REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 55.17 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.74 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 21% PEG 4000, 0.1M ACETATE BUFFER, PH REMARK 280 5.6, VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K 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 20.03500 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 56.89000 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 21.21000 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 56.89000 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 20.03500 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 21.21000 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 480 REMARK 480 ZERO OCCUPANCY ATOM REMARK 480 THE FOLLOWING RESIDUES HAVE ATOMS MODELED WITH ZERO REMARK 480 OCCUPANCY. THE LOCATION AND PROPERTIES OF THESE ATOMS REMARK 480 MAY NOT BE RELIABLE. (M=MODEL NUMBER; RES=RESIDUE NAME; REMARK 480 C=CHAIN IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE): REMARK 480 M RES C SSEQI ATOMS REMARK 480 THR A 90 CB OG1 CG2 REMARK 480 LYS A 110 CD CE NZ REMARK 480 GLU A 111 CG CD OE1 OE2 REMARK 480 ASP A 125 CG OD1 OD2 REMARK 480 LEU A 126 CG CD1 CD2 REMARK 480 GLU A 127 CB CG CD OE1 OE2 REMARK 480 LYS A 160 NZ REMARK 480 ILE A 162 CB CG1 CG2 CD1 OXT 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 2349 O HOH A 2370 0.20 REMARK 500 O HOH A 2380 O HOH A 2385 1.83 REMARK 500 O ALA A 15 O HOH A 2353 2.17 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 SER A 2 -160.77 -52.25 REMARK 500 GLU A 10 18.57 53.72 REMARK 500 TYR A 71 -17.14 81.26 REMARK 500 SER A 74 62.39 -68.74 REMARK 500 ASP A 85 0.35 -68.58 REMARK 500 THR A 90 -16.90 -32.79 REMARK 500 PRO A 95 -165.57 -65.29 REMARK 500 PRO A 124 161.53 -37.48 REMARK 500 ASP A 125 42.49 -99.82 REMARK 500 LEU A 126 -17.56 -39.71 REMARK 500 REMARK 500 REMARK: NULL REMARK 800 REMARK 800 SITE REMARK 800 SITE_IDENTIFIER: AC1 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 3PH A 2341 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 1G13 RELATED DB: PDB REMARK 900 APO STRUCTURE, DIFFERENT CRYSTAL FORM REMARK 900 RELATED ID: 1PU5 RELATED DB: PDB REMARK 900 CO-CRYSTAL WITH GM2 BOUND DBREF 1PUB A 1 162 UNP P17900 SAP3_HUMAN 39 200 SEQRES 1 A 162 SER SER PHE SER TRP ASP ASN CYS ASP GLU GLY LYS ASP SEQRES 2 A 162 PRO ALA VAL ILE ARG SER LEU THR LEU GLU PRO ASP PRO SEQRES 3 A 162 ILE ILE VAL PRO GLY ASN VAL THR LEU SER VAL MET GLY SEQRES 4 A 162 SER THR SER VAL PRO LEU SER SER PRO LEU LYS VAL ASP SEQRES 5 A 162 LEU VAL LEU GLU LYS GLU VAL ALA GLY LEU TRP ILE LYS SEQRES 6 A 162 ILE PRO CYS THR ASP TYR ILE GLY SER CYS THR PHE GLU SEQRES 7 A 162 HIS PHE CYS ASP VAL LEU ASP MET LEU ILE PRO THR GLY SEQRES 8 A 162 GLU PRO CYS PRO GLU PRO LEU ARG THR TYR GLY LEU PRO SEQRES 9 A 162 CYS HIS CYS PRO PHE LYS GLU GLY THR TYR SER LEU PRO SEQRES 10 A 162 LYS SER GLU PHE VAL VAL PRO ASP LEU GLU LEU PRO SER SEQRES 11 A 162 TRP LEU THR THR GLY ASN TYR ARG ILE GLU SER VAL LEU SEQRES 12 A 162 SER SER SER GLY LYS ARG LEU GLY CYS ILE LYS ILE ALA SEQRES 13 A 162 ALA SER LEU LYS GLY ILE HET 3PH A2341 48 HETNAM 3PH 1,2-DIACYL-GLYCEROL-3-SN-PHOSPHATE HETSYN 3PH PHOSPHATIDIC ACID FORMUL 2 3PH C39 H77 O8 P FORMUL 3 HOH *61(H2 O) HELIX 1 1 ASP A 9 LYS A 12 5 4 HELIX 2 2 HIS A 79 ILE A 88 1 10 HELIX 3 3 PRO A 129 THR A 134 1 6 SHEET 1 A 5 SER A 4 ASN A 7 0 SHEET 2 A 5 LYS A 148 GLY A 161 -1 O ALA A 156 N SER A 4 SHEET 3 A 5 GLY A 135 SER A 145 -1 N ILE A 139 O ILE A 155 SHEET 4 A 5 LYS A 50 VAL A 59 -1 N GLU A 56 O ARG A 138 SHEET 5 A 5 LEU A 62 LYS A 65 -1 O ILE A 64 N LYS A 57 SHEET 1 B 5 ILE A 27 VAL A 29 0 SHEET 2 B 5 LYS A 148 GLY A 161 1 O SER A 158 N ILE A 27 SHEET 3 B 5 GLY A 135 SER A 145 -1 N ILE A 139 O ILE A 155 SHEET 4 B 5 LYS A 50 VAL A 59 -1 N GLU A 56 O ARG A 138 SHEET 5 B 5 THR A 76 PHE A 77 -1 O PHE A 77 N VAL A 51 SHEET 1 C 3 ALA A 15 GLU A 23 0 SHEET 2 C 3 GLY A 31 THR A 41 -1 O MET A 38 N SER A 19 SHEET 3 C 3 GLY A 112 VAL A 123 -1 O VAL A 123 N GLY A 31 SSBOND 1 CYS A 8 CYS A 152 1555 1555 2.00 SSBOND 2 CYS A 68 CYS A 75 1555 1555 2.02 SSBOND 3 CYS A 81 CYS A 107 1555 1555 2.02 SSBOND 4 CYS A 94 CYS A 105 1555 1555 2.03 CISPEP 1 GLU A 23 PRO A 24 0 -0.06 CISPEP 2 ASP A 25 PRO A 26 0 0.03 CISPEP 3 VAL A 29 PRO A 30 0 0.05 CISPEP 4 SER A 47 PRO A 48 0 0.45 CISPEP 5 GLU A 96 PRO A 97 0 0.11 CISPEP 6 CYS A 107 PRO A 108 0 0.50 SITE 1 AC1 7 ILE A 27 VAL A 37 SER A 141 ILE A 153 SITE 2 AC1 7 ILE A 155 LEU A 159 HOH A2368 CRYST1 40.070 42.420 113.780 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 0.024956 0.000000 0.000000 0.00000 SCALE2 0.000000 0.023574 0.000000 0.00000 SCALE3 0.000000 0.000000 0.008789 0.00000