HEADER TRANSPORT PROTEIN 27-OCT-09 3KFI TITLE MAJOR MOUSE URINARY PROTEIN IV COMPLEXED WITH 2,5-DIMETHYLPYRAZINE COMPND MOL_ID: 1; COMPND 2 MOLECULE: MAJOR URINARY PROTEIN 4; COMPND 3 CHAIN: A; COMPND 4 SYNONYM: MUP 4; COMPND 5 ENGINEERED: YES SOURCE MOL_ID: 1; SOURCE 2 ORGANISM_SCIENTIFIC: MUS MUSCULUS; SOURCE 3 ORGANISM_COMMON: MOUSE; SOURCE 4 ORGANISM_TAXID: 10090; SOURCE 5 GENE: MUP4; SOURCE 6 EXPRESSION_SYSTEM: ESCHERICHIA COLI; SOURCE 7 EXPRESSION_SYSTEM_TAXID: 562; SOURCE 8 EXPRESSION_SYSTEM_STRAIN: BL21(DE3); SOURCE 9 EXPRESSION_SYSTEM_VECTOR_TYPE: PLASMID; SOURCE 10 EXPRESSION_SYSTEM_PLASMID: PET28A KEYWDS PHEROMONE, MAJOR URINARY PROTEIN, LIPOCALIN, BETA BARREL, DISULFIDE KEYWDS 2 BOND, PHEROMONE-BINDING, SECRETED, TRANSPORT, TRANSPORT PROTEIN EXPDTA X-RAY DIFFRACTION AUTHOR S.PEREZ-MILLER,Q.ZOU,T.D.HURLEY REVDAT 4 06-SEP-23 3KFI 1 REMARK REVDAT 3 01-NOV-17 3KFI 1 REMARK REVDAT 2 11-AUG-10 3KFI 1 JRNL REVDAT 1 16-JUN-10 3KFI 0 JRNL AUTH S.PEREZ-MILLER,Q.ZOU,M.V.NOVOTNY,T.D.HURLEY JRNL TITL HIGH RESOLUTION X-RAY STRUCTURES OF MOUSE MAJOR URINARY JRNL TITL 2 PROTEIN NASAL ISOFORM IN COMPLEX WITH PHEROMONES. JRNL REF PROTEIN SCI. V. 19 1469 2010 JRNL REFN ISSN 0961-8368 JRNL PMID 20509168 JRNL DOI 10.1002/PRO.426 REMARK 2 REMARK 2 RESOLUTION. 1.42 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) : 1.42 REMARK 3 RESOLUTION RANGE LOW (ANGSTROMS) : 17.80 REMARK 3 DATA CUTOFF (SIGMA(F)) : NULL REMARK 3 COMPLETENESS FOR RANGE (%) : 95.0 REMARK 3 NUMBER OF REFLECTIONS : 27604 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) : 0.150 REMARK 3 R VALUE (WORKING SET) : 0.148 REMARK 3 FREE R VALUE : 0.181 REMARK 3 FREE R VALUE TEST SET SIZE (%) : 5.000 REMARK 3 FREE R VALUE TEST SET COUNT : 1464 REMARK 3 REMARK 3 NUMBER OF NON-HYDROGEN ATOMS USED IN REFINEMENT. REMARK 3 PROTEIN ATOMS : 1247 REMARK 3 NUCLEIC ACID ATOMS : 0 REMARK 3 HETEROGEN ATOMS : 10 REMARK 3 SOLVENT ATOMS : 232 REMARK 3 REMARK 3 B VALUES. REMARK 3 FROM WILSON PLOT (A**2) : 20.60 REMARK 3 MEAN B VALUE (OVERALL, A**2) : 19.05 REMARK 3 OVERALL ANISOTROPIC B VALUE. REMARK 3 B11 (A**2) : -0.27000 REMARK 3 B22 (A**2) : 0.00000 REMARK 3 B33 (A**2) : 0.00000 REMARK 3 B12 (A**2) : -0.53000 REMARK 3 B13 (A**2) : 0.80000 REMARK 3 B23 (A**2) : 0.00000 REMARK 3 REMARK 3 ESTIMATED OVERALL COORDINATE ERROR. REMARK 3 ESU BASED ON R VALUE (A): NULL 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) : 0.015 ; 0.022 REMARK 3 ANGLE DISTANCE (A) : NULL ; 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 3KFI COMPLIES WITH FORMAT V. 3.30, 13-JUL-11 REMARK 100 REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 06-NOV-09. REMARK 100 THE DEPOSITION ID IS D_1000055927. REMARK 200 REMARK 200 EXPERIMENTAL DETAILS REMARK 200 EXPERIMENT TYPE : X-RAY DIFFRACTION REMARK 200 DATE OF DATA COLLECTION : 06-OCT-03 REMARK 200 TEMPERATURE (KELVIN) : 100 REMARK 200 PH : 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 RU200 REMARK 200 MONOCHROMATIC OR LAUE (M/L) : M REMARK 200 WAVELENGTH OR RANGE (A) : 1.54 REMARK 200 MONOCHROMATOR : OSMIC CONFOCAL REMARK 200 OPTICS : NULL REMARK 200 REMARK 200 DETECTOR TYPE : IMAGE PLATE REMARK 200 DETECTOR MANUFACTURER : RIGAKU RAXIS IV REMARK 200 INTENSITY-INTEGRATION SOFTWARE : DENZO REMARK 200 DATA SCALING SOFTWARE : SCALEPACK REMARK 200 REMARK 200 NUMBER OF UNIQUE REFLECTIONS : 29102 REMARK 200 RESOLUTION RANGE HIGH (A) : 1.420 REMARK 200 RESOLUTION RANGE LOW (A) : 50.000 REMARK 200 REJECTION CRITERIA (SIGMA(I)) : 0.200 REMARK 200 REMARK 200 OVERALL. REMARK 200 COMPLETENESS FOR RANGE (%) : 95.1 REMARK 200 DATA REDUNDANCY : 2.900 REMARK 200 R MERGE (I) : 0.05400 REMARK 200 R SYM (I) : NULL REMARK 200 FOR THE DATA SET : 16.3000 REMARK 200 REMARK 200 IN THE HIGHEST RESOLUTION SHELL. REMARK 200 HIGHEST RESOLUTION SHELL, RANGE HIGH (A) : 1.42 REMARK 200 HIGHEST RESOLUTION SHELL, RANGE LOW (A) : 1.47 REMARK 200 COMPLETENESS FOR SHELL (%) : 83.2 REMARK 200 DATA REDUNDANCY IN SHELL : 1.70 REMARK 200 R MERGE FOR SHELL (I) : 0.27700 REMARK 200 R SYM FOR SHELL (I) : NULL REMARK 200 FOR SHELL : 2.400 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: MUP-I (PDB ENTRY 1I06) REMARK 200 REMARK 200 REMARK: NULL REMARK 280 REMARK 280 CRYSTAL REMARK 280 SOLVENT CONTENT, VS (%): 41.01 REMARK 280 MATTHEWS COEFFICIENT, VM (ANGSTROMS**3/DA): 2.09 REMARK 280 REMARK 280 CRYSTALLIZATION CONDITIONS: 0.2-0.5 M CALCIUM CHLORIDE DIHYDRATE, REMARK 280 20% (W/V) POLYETHYLENE GLYCOL 3350, PH 6, VAPOR DIFFUSION, REMARK 280 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 23.91900 REMARK 290 SMTRY2 2 0.000000 -1.000000 0.000000 0.00000 REMARK 290 SMTRY3 2 0.000000 0.000000 1.000000 30.73950 REMARK 290 SMTRY1 3 -1.000000 0.000000 0.000000 0.00000 REMARK 290 SMTRY2 3 0.000000 1.000000 0.000000 26.72200 REMARK 290 SMTRY3 3 0.000000 0.000000 -1.000000 30.73950 REMARK 290 SMTRY1 4 1.000000 0.000000 0.000000 23.91900 REMARK 290 SMTRY2 4 0.000000 -1.000000 0.000000 26.72200 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 SOFTWARE DETERMINED QUATERNARY STRUCTURE: MONOMERIC REMARK 350 SOFTWARE USED: PISA 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 GLU A 1 REMARK 465 GLU A 2 REMARK 465 ALA A 3 REMARK 465 THR A 4 REMARK 465 SER A 5 REMARK 465 LYS A 6 REMARK 465 GLY A 7 REMARK 465 GLN A 8 REMARK 465 ASN A 9 REMARK 465 GLU A 162 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 LYS A 28 CE NZ REMARK 480 LYS A 136 CD CE NZ 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 OE1 GLU A 132 O HOH A 731 2.05 REMARK 500 ND2 ASN A 50 O HOH A 659 2.07 REMARK 500 O HOH A 591 O HOH A 658 2.12 REMARK 500 O HOH A 607 O HOH A 720 2.13 REMARK 500 O HOH A 592 O HOH A 661 2.17 REMARK 500 O HOH A 725 O HOH A 733 2.17 REMARK 500 NZ LYS A 136 O HOH A 588 2.19 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 TYR A 84 113.89 -166.47 REMARK 500 TYR A 97 -44.60 70.44 REMARK 500 ASN A 99 -53.08 -134.63 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 CL A 201 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC2 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE CL A 202 REMARK 800 REMARK 800 SITE_IDENTIFIER: AC3 REMARK 800 EVIDENCE_CODE: SOFTWARE REMARK 800 SITE_DESCRIPTION: BINDING SITE FOR RESIDUE 25R A 301 REMARK 900 REMARK 900 RELATED ENTRIES REMARK 900 RELATED ID: 3KFF RELATED DB: PDB REMARK 900 MAJOR MOUSE URINARY PROTEIN IV COMPLEXED WITH 2-SEC-BUTYL-4,5- REMARK 900 DIHYDROTHIAZOLE REMARK 900 RELATED ID: 3KFG RELATED DB: PDB REMARK 900 MAJOR MOUSE URINARY PROTEIN IV COMPLEXED WITH 2-HEPTANONE REMARK 900 RELATED ID: 3KFH RELATED DB: PDB REMARK 900 MAJOR MOUSE URINARY PROTEIN IV COMPLEXED WITH 2-ETHYLHEXANOL DBREF 3KFI A 1 162 UNP P11590 MUP4_MOUSE 17 178 SEQRES 1 A 162 GLU GLU ALA THR SER LYS GLY GLN ASN LEU ASN VAL GLU SEQRES 2 A 162 LYS ILE ASN GLY GLU TRP PHE SER ILE LEU LEU ALA SER SEQRES 3 A 162 ASP LYS ARG GLU LYS ILE GLU GLU HIS GLY SER MET ARG SEQRES 4 A 162 VAL PHE VAL GLU HIS ILE HIS VAL LEU GLU ASN SER LEU SEQRES 5 A 162 ALA PHE LYS PHE HIS THR VAL ILE ASP GLY GLU CYS SER SEQRES 6 A 162 GLU ILE PHE LEU VAL ALA ASP LYS THR GLU LYS ALA GLY SEQRES 7 A 162 GLU TYR SER VAL MET TYR ASP GLY PHE ASN THR PHE THR SEQRES 8 A 162 ILE LEU LYS THR ASP TYR ASP ASN TYR ILE MET PHE HIS SEQRES 9 A 162 LEU ILE ASN GLU LYS ASP GLY LYS THR PHE GLN LEU MET SEQRES 10 A 162 GLU LEU TYR GLY ARG LYS ALA ASP LEU ASN SER ASP ILE SEQRES 11 A 162 LYS GLU LYS PHE VAL LYS LEU CYS GLU GLU HIS GLY ILE SEQRES 12 A 162 ILE LYS GLU ASN ILE ILE ASP LEU THR LYS THR ASN ARG SEQRES 13 A 162 CYS LEU LYS ALA ARG GLU HET CL A 201 1 HET CL A 202 1 HET 25R A 301 8 HETNAM CL CHLORIDE ION HETNAM 25R 2,5-DIMETHYLPYRAZINE FORMUL 2 CL 2(CL 1-) FORMUL 4 25R C6 H8 N2 FORMUL 5 HOH *232(H2 O) HELIX 1 1 ASN A 11 ASN A 16 5 6 HELIX 2 2 LYS A 28 ILE A 32 5 5 HELIX 3 3 ASN A 127 GLU A 140 1 14 HELIX 4 4 ILE A 144 GLU A 146 5 3 HELIX 5 5 THR A 152 THR A 154 5 3 HELIX 6 6 CYS A 157 ARG A 161 5 5 SHEET 1 A10 GLY A 17 GLU A 18 0 SHEET 2 A10 VAL A 40 LEU A 48 -1 O ILE A 45 N GLY A 17 SHEET 3 A10 SER A 51 ILE A 60 -1 O LYS A 55 N GLU A 43 SHEET 4 A10 GLU A 63 LYS A 73 -1 O ILE A 67 N PHE A 56 SHEET 5 A10 TYR A 80 MET A 83 -1 O SER A 81 N ASP A 72 SHEET 6 A10 PHE A 87 THR A 95 -1 O ASN A 88 N VAL A 82 SHEET 7 A10 TYR A 100 LYS A 109 -1 O ILE A 106 N THR A 89 SHEET 8 A10 LYS A 112 GLY A 121 -1 O LEU A 116 N LEU A 105 SHEET 9 A10 PHE A 20 SER A 26 -1 N ALA A 25 O MET A 117 SHEET 10 A10 ILE A 148 ASP A 150 -1 O ILE A 149 N LEU A 24 SSBOND 1 CYS A 64 CYS A 157 1555 1555 2.05 SITE 1 AC1 2 ARG A 156 LEU A 158 SITE 1 AC2 2 HIS A 44 PHE A 68 SITE 1 AC3 3 PHE A 56 GLU A 118 TYR A 120 CRYST1 47.838 53.444 61.479 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 0.020904 0.000000 0.000000 0.00000 SCALE2 0.000000 0.018711 0.000000 0.00000 SCALE3 0.000000 0.000000 0.016266 0.00000