HEADER TRANSFERASE 14-APR-05 1ZD8 TITLE STRUCTURE OF HUMAN ADENYLATE KINASE 3 LIKE 1 COMPND MOL_ID: 1; COMPND 2 MOLECULE: GTP:AMP PHOSPHOTRANSFERASE MITOCHONDRIAL; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: AK3, ADENYLATE KINASE 3 ALPHA LIKE 1; COMPND 5 EC: 2.7.4.10; COMPND 6 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: HOMO SAPIENS; SOURCE 3 ORGANISM_COMMON: HUMAN; SOURCE 4 ORGANISM_TAXID: 9606; SOURCE 5 GENE: AK3L1, AKL3L; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI BL21(DE3); SOURCE 7 EXPRESSION_SYSTEM_TAXID: 469008; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28 KEYWDS ATP:AMP PHOSPHOTRANSFERASE, MYOKINASE, STRUCTURAL GENOMICS, KEYWDS 2 STRUCTURAL GENOMICS CONSORTIUM, SGC, TRANSFERASE EXPDTA X-RAY DIFFRACTION AUTHOR J.CHOE,A.ATANASSOVA,C.ARROWSMITH,A.EDWARDS,M.SUNDSTROM,A.BOCHKAREV, AUTHOR 2 H.PARK,STRUCTURAL GENOMICS CONSORTIUM (SGC) REVDAT 3 23-AUG-23 1ZD8 1 REMARK REVDAT 2 24-FEB-09 1ZD8 1 VERSN REVDAT 1 17-MAY-05 1ZD8 0 JRNL AUTH A.ATANASSOVA,J.CHOE,C.ARROWSMITH,A.EDWARDS,M.SUNDSTROM, JRNL AUTH 2 A.BOCHKAREV,H.PARK JRNL TITL STRUCTURE OF HUMAN ADENYLATE KINASE 3 LIKE 1 JRNL REF TO BE PUBLISHED JRNL REFN REMARK 2 REMARK 2 RESOLUTION. 1.48 ANGSTROMS. REMARK 3 REMARK 3 REFINEMENT. REMARK 3 PROGRAM : REFMAC 5.2.0005 REMARK 3 AUTHORS : MURSHUDOV,SKUBAK,LEBEDEV,PANNU,STEINER, REMARK 3 : NICHOLLS,WINN,LONG,VAGIN REMARK 3 REMARK 3 REFINEMENT TARGET : MAXIMUM LIKELIHOOD REMARK 3 REMARK 3 DATA USED IN REFINEMENT. REMARK 3 RESOLUTION RANGE HIGH (ANGSTROMS) : 1.48 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 47.67 REMARK 3 DATA CUTOFF (SIGMA(F)) : 0.000 REMARK 3 COMPLETENESS FOR RANGE (%) : 96.9 REMARK 3 NUMBER OF REFLECTIONS : 37693 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) : 0.225 REMARK 3 R VALUE (WORKING SET) : 0.224 REMARK 3 FREE R VALUE : 0.240 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1994 REMARK 3 REMARK 3 FIT IN THE HIGHEST RESOLUTION BIN. REMARK 3 TOTAL NUMBER OF BINS USED : 20 REMARK 3 BIN RESOLUTION RANGE HIGH (A) : 1.48 REMARK 3 BIN RESOLUTION RANGE LOW (A) : 1.52 REMARK 3 REFLECTION IN BIN (WORKING SET) : 2543 REMARK 3 BIN COMPLETENESS (WORKING+TEST) (%) : 88.19 REMARK 3 BIN R VALUE (WORKING SET) : 0.2760 REMARK 3 BIN FREE R VALUE SET COUNT : 124 REMARK 3 BIN FREE R VALUE : 0.3200 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1697 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 0 REMARK 3 SOLVENT ATOMS : 225 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 19.30 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.39 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : 0.57000 REMARK 3 B22 (A**2) : -0.21000 REMARK 3 B33 (A**2) : -0.44000 REMARK 3 B12 (A**2) : 0.00000 REMARK 3 B13 (A**2) : -0.13000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): 0.086 REMARK 3 ESU BASED ON FREE R VALUE (A): 0.082 REMARK 3 ESU BASED ON MAXIMUM LIKELIHOOD (A): 0.050 REMARK 3 ESU FOR B VALUES BASED ON MAXIMUM LIKELIHOOD (A**2): 1.283 REMARK 3 REMARK 3 CORRELATION COEFFICIENTS. REMARK 3 CORRELATION COEFFICIENT FO-FC : 0.936 REMARK 3 CORRELATION COEFFICIENT FO-FC FREE : 0.930 REMARK 3 REMARK 3 RMS DEVIATIONS FROM IDEAL VALUES COUNT RMS WEIGHT REMARK 3 BOND LENGTHS REFINED ATOMS (A): 1734 ; 0.010 ; 0.022 REMARK 3 BOND LENGTHS OTHERS (A): NULL ; NULL ; NULL REMARK 3 BOND ANGLES REFINED ATOMS (DEGREES): 2354 ; 1.282 ; 1.979 REMARK 3 BOND ANGLES OTHERS (DEGREES): NULL ; NULL ; NULL REMARK 3 TORSION ANGLES, PERIOD 1 (DEGREES): 211 ; 5.275 ; 5.000 REMARK 3 TORSION ANGLES, PERIOD 2 (DEGREES): 77 ;36.521 ;24.026 REMARK 3 TORSION ANGLES, PERIOD 3 (DEGREES): 310 ;11.948 ;15.000 REMARK 3 TORSION ANGLES, PERIOD 4 (DEGREES): 12 ;14.323 ;15.000 REMARK 3 CHIRAL-CENTER RESTRAINTS (A**3): 268 ; 0.082 ; 0.200 REMARK 3 GENERAL PLANES REFINED ATOMS (A): 1295 ; 0.005 ; 0.020 REMARK 3 GENERAL PLANES OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED CONTACTS REFINED ATOMS (A): 784 ; 0.206 ; 0.200 REMARK 3 NON-BONDED CONTACTS OTHERS (A): NULL ; NULL ; NULL REMARK 3 NON-BONDED TORSION REFINED ATOMS (A): 1196 ; 0.307 ; 0.200 REMARK 3 NON-BONDED TORSION OTHERS (A): NULL ; NULL ; NULL REMARK 3 H-BOND (X...Y) REFINED ATOMS (A): 132 ; 0.116 ; 0.200 REMARK 3 H-BOND (X...Y) OTHERS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 POTENTIAL METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY VDW REFINED ATOMS (A): 28 ; 0.180 ; 0.200 REMARK 3 SYMMETRY VDW OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY H-BOND REFINED ATOMS (A): 15 ; 0.120 ; 0.200 REMARK 3 SYMMETRY H-BOND OTHERS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION REFINED ATOMS (A): NULL ; NULL ; NULL REMARK 3 SYMMETRY METAL-ION OTHERS (A): NULL ; NULL ; NULL REMARK 3 REMARK 3 ISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 MAIN-CHAIN BOND REFINED ATOMS (A**2): 1089 ; 0.889 ; 1.500 REMARK 3 MAIN-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 MAIN-CHAIN ANGLE REFINED ATOMS (A**2): 1723 ; 1.405 ; 2.000 REMARK 3 MAIN-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN BOND REFINED ATOMS (A**2): 726 ; 2.290 ; 3.000 REMARK 3 SIDE-CHAIN BOND OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SIDE-CHAIN ANGLE REFINED ATOMS (A**2): 631 ; 3.476 ; 4.500 REMARK 3 SIDE-CHAIN ANGLE OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B REFINED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 LONG RANGE B OTHER ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 ANISOTROPIC THERMAL FACTOR RESTRAINTS. COUNT RMS WEIGHT REMARK 3 RIGID-BOND RESTRAINTS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; FREE ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 SPHERICITY; BONDED ATOMS (A**2): NULL ; NULL ; NULL REMARK 3 REMARK 3 NCS RESTRAINTS STATISTICS REMARK 3 NUMBER OF DIFFERENT NCS GROUPS : NULL REMARK 3 REMARK 3 TLS DETAILS REMARK 3 NUMBER OF TLS GROUPS : NULL REMARK 3 REMARK 3 BULK SOLVENT MODELLING. REMARK 3 METHOD USED : MASK REMARK 3 PARAMETERS FOR MASK CALCULATION REMARK 3 VDW PROBE RADIUS : 1.20 REMARK 3 ION PROBE RADIUS : 0.80 REMARK 3 SHRINKAGE RADIUS : 0.80 REMARK 3 REMARK 3 OTHER REFINEMENT REMARKS: HYDROGENS HAVE BEEN ADDED IN THE RIDING REMARK 3 POSITIONS REMARK 4 REMARK 4 1ZD8 COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 15-APR-05. REMARK 100 THE DEPOSITION ID IS D_1000032593. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 09-APR-05 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 7.5 REMARK 200 NUMBER OF CRYSTALS USED : 1 REMARK 200 REMARK 200 SYNCHROTRON (Y/N) : Y REMARK 200 RADIATION SOURCE : APS REMARK 200 BEAMLINE : 32-ID REMARK 200 X-RAY GENERATOR MODEL : NULL REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.0 REMARK 200 MONOCHROMATOR : DIAMOND 111 REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : CCD REMARK 200 DETECTOR MANUFACTURER : MARRESEARCH REMARK 200 INTENSITY-INTEGRATION SOFTWARE : HKL-2000 REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 39687 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.480 REMARK 200 RESOLUTION RANGE LOW (A) : 47.670 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 1.000 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 96.2 REMARK 200 DATA REDUNDANCY : 3.800 REMARK 200 R MERGE (I) : 0.05300 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) : 1.48 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.53 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.6 REMARK 200 DATA REDUNDANCY IN SHELL : 3.10 REMARK 200 R MERGE FOR SHELL (I) : 0.24200 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: AMORE REMARK 200 STARTING MODEL: PDB ENTRY 1AKY REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 52.10 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.60 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: PEG 4000, HEPES, PH 7.5, VAPOR REMARK 280 DIFFUSION, SITTING DROP, TEMPERATURE 291K REMARK 290 REMARK 290 CRYSTALLOGRAPHIC SYMMETRY REMARK 290 SYMMETRY OPERATORS FOR SPACE GROUP: P 1 21 1 REMARK 290 REMARK 290 SYMOP SYMMETRY REMARK 290 NNNMMM OPERATOR REMARK 290 1555 X,Y,Z REMARK 290 2555 -X,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 30.93650 REMARK 290 SMTRY3 2 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 0 REMARK 465 GLY A 1 REMARK 465 ALA A 2 REMARK 465 SER A 3 REMARK 465 ALA A 4 REMARK 465 ARG A 5 REMARK 465 ARG A 218 REMARK 465 SER A 219 REMARK 465 GLN A 220 REMARK 465 LYS A 221 REMARK 465 ALA A 222 REMARK 465 SER A 223 REMARK 465 VAL A 224 REMARK 465 THR A 225 REMARK 465 PRO A 226 DBREF 1ZD8 A 0 226 UNP Q9UIJ7 KAD3_HUMAN 0 226 SEQRES 1 A 227 MET GLY ALA SER ALA ARG LEU LEU ARG ALA VAL ILE MET SEQRES 2 A 227 GLY ALA PRO GLY SER GLY LYS GLY THR VAL SER SER ARG SEQRES 3 A 227 ILE THR THR HIS PHE GLU LEU LYS HIS LEU SER SER GLY SEQRES 4 A 227 ASP LEU LEU ARG ASP ASN MET LEU ARG GLY THR GLU ILE SEQRES 5 A 227 GLY VAL LEU ALA LYS ALA PHE ILE ASP GLN GLY LYS LEU SEQRES 6 A 227 ILE PRO ASP ASP VAL MET THR ARG LEU ALA LEU HIS GLU SEQRES 7 A 227 LEU LYS ASN LEU THR GLN TYR SER TRP LEU LEU ASP GLY SEQRES 8 A 227 PHE PRO ARG THR LEU PRO GLN ALA GLU ALA LEU ASP ARG SEQRES 9 A 227 ALA TYR GLN ILE ASP THR VAL ILE ASN LEU ASN VAL PRO SEQRES 10 A 227 PHE GLU VAL ILE LYS GLN ARG LEU THR ALA ARG TRP ILE SEQRES 11 A 227 HIS PRO ALA SER GLY ARG VAL TYR ASN ILE GLU PHE ASN SEQRES 12 A 227 PRO PRO LYS THR VAL GLY ILE ASP ASP LEU THR GLY GLU SEQRES 13 A 227 PRO LEU ILE GLN ARG GLU ASP ASP LYS PRO GLU THR VAL SEQRES 14 A 227 ILE LYS ARG LEU LYS ALA TYR GLU ASP GLN THR LYS PRO SEQRES 15 A 227 VAL LEU GLU TYR TYR GLN LYS LYS GLY VAL LEU GLU THR SEQRES 16 A 227 PHE SER GLY THR GLU THR ASN LYS ILE TRP PRO TYR VAL SEQRES 17 A 227 TYR ALA PHE LEU GLN THR LYS VAL PRO GLN ARG SER GLN SEQRES 18 A 227 LYS ALA SER VAL THR PRO FORMUL 2 HOH *225(H2 O) HELIX 1 1 GLY A 18 PHE A 30 1 13 HELIX 2 2 SER A 37 GLY A 48 1 12 HELIX 3 3 THR A 49 ASP A 60 1 12 HELIX 4 4 PRO A 66 ASN A 80 1 15 HELIX 5 5 THR A 94 ARG A 103 1 10 HELIX 6 6 PRO A 116 THR A 125 1 10 HELIX 7 7 ARG A 160 ASP A 163 5 4 HELIX 8 8 LYS A 164 LYS A 189 1 26 HELIX 9 9 GLU A 199 GLN A 212 1 14 SHEET 1 A 5 LYS A 33 SER A 36 0 SHEET 2 A 5 TRP A 86 ASP A 89 1 O ASP A 89 N LEU A 35 SHEET 3 A 5 ARG A 8 GLY A 13 1 N ALA A 9 O LEU A 88 SHEET 4 A 5 THR A 109 ASN A 114 1 O ILE A 111 N VAL A 10 SHEET 5 A 5 LEU A 192 SER A 196 1 O GLU A 193 N VAL A 110 SHEET 1 B 2 ARG A 127 HIS A 130 0 SHEET 2 B 2 ARG A 135 ASN A 138 -1 O TYR A 137 N TRP A 128 CISPEP 1 PHE A 91 PRO A 92 0 2.14 CRYST1 42.128 61.873 50.192 90.00 108.14 90.00 P 1 21 1 2 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 0.023737 0.000000 0.007777 0.00000 SCALE2 0.000000 0.016162 0.000000 0.00000 SCALE3 0.000000 0.000000 0.020966 0.00000